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Article ; Online: The active site of the SGNH hydrolase-like fold proteins

Konstantin Denessiouk / Alexander I. Denesyuk / Sergei E. Permyakov / Eugene A. Permyakov / Mark S. Johnson / Vladimir N. Uversky

Current Research in Structural Biology, Vol 7, Iss , Pp 100123- (2024)

Nucleophile–oxyanion (Nuc-Oxy) and Acid–Base zones

2024

Abstract: SGNH hydrolase-like fold proteins are serine proteases with the default Asp-His-Ser catalytic triad. Here, we show that these proteins share two unique conserved structural organizations around the active site: (1) the Nuc-Oxy Zone around the catalytic ... ...

Abstract	SGNH hydrolase-like fold proteins are serine proteases with the default Asp-His-Ser catalytic triad. Here, we show that these proteins share two unique conserved structural organizations around the active site: (1) the Nuc-Oxy Zone around the catalytic nucleophile and the oxyanion hole, and (2) the Acid-Base Zone around the catalytic acid and base. The Nuc-Oxy Zone consists of 14 amino acids cross-linked with eight conserved intra- and inter-block hydrogen bonds. The Acid–Base Zone is constructed from a single fragment of the polypeptide chain, which incorporates both the catalytic acid and base, and whose N- and C-terminal residues are linked together by a conserved hydrogen bond. The Nuc-Oxy and Acid-Base Zones are connected by an SHLink, a two-bond conserved interaction from amino acids, adjacent to the catalytic nucleophile and base.
Keywords	SGNH-Hydrolases ; Catalytic triad ; Oxyanion hole ; Nuc–Oxy and Acid–Base zones ; SHLink ; Biology (General) ; QH301-705.5
Subject code	540
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: The active site of the SGNH hydrolase-like fold proteins: Nucleophile-oxyanion (Nuc-Oxy) and Acid-Base zones.

Denessiouk, Konstantin / Denesyuk, Alexander I / Permyakov, Sergei E / Permyakov, Eugene A / Johnson, Mark S / Uversky, Vladimir N

Current research in structural biology

2023 Volume 7, Page(s) 100123

Abstract	SGNH hydrolase-like fold proteins are serine proteases with the default Asp-His-Ser catalytic triad. Here, we show that these proteins share two unique conserved structural organizations around the active site: (1) the Nuc-Oxy Zone around the catalytic nucleophile and the oxyanion hole, and (2) the Acid-Base Zone around the catalytic acid and base. The Nuc-Oxy Zone consists of 14 amino acids cross-linked with eight conserved intra- and inter-block hydrogen bonds. The Acid-Base Zone is constructed from a single fragment of the polypeptide chain, which incorporates both the catalytic acid and base, and whose N- and C-terminal residues are linked together by a conserved hydrogen bond. The Nuc-Oxy and Acid-Base Zones are connected by an SHLink, a two-bond conserved interaction from amino acids, adjacent to the catalytic nucleophile and base.
Language	English
Publishing date	2023-12-29
Publishing country	Netherlands
Document type	Journal Article
ISSN	2665-928X
ISSN (online)	2665-928X
DOI	10.1016/j.crstbi.2023.100123
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Article ; Online: Canonical structural-binding modes in the calmodulin-target protein complexes.

Denesyuk, Alexander I / Permyakov, Sergei E / Permyakov, Eugene A / Johnson, Mark S / Denessiouk, Konstantin / Uversky, Vladimir N

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 16, Page(s) 7582–7594

Abstract: Intracellular calcium sensor protein calmodulin (CaM) belongs to the large EF-hand protein superfamily. CaM shows a unique and not fully understood ability to bind to multiple targets, allows them to participate in a variety of regulatory processes. The ... ...

Abstract	Intracellular calcium sensor protein calmodulin (CaM) belongs to the large EF-hand protein superfamily. CaM shows a unique and not fully understood ability to bind to multiple targets, allows them to participate in a variety of regulatory processes. The protein has two approximately symmetrical globular domains (the N- and C-lobes). Analysis of the CaM-binding sites of target proteins showed that they have two hydrophobic 'anchor' amino acids separated by 10 to 17 residues. Consequently, several CaM-binding motifs: {1-10}, {1-11}, {1-13}, {1-14}, {1-16}, {1-17}, differing by the distance between the two anchor residues along the amino acid sequence, have been identified. Despite extensive structural information on the role of target-protein amino acid residues in the formation of complexes with CaM, much less is known about the role of amino acids from CaM contributing to these interactions. In this work, a quantitative analysis of the contact surfaces of CaM and target proteins has been carried out for 35 representative three-dimensional structures. It has been shown that, in addition to the two hydrophobic terminal residues of the target fragment, the interaction also involves residues that are 4 residues earlier in the sequence (binding mode {1-5}). It has also been found that the N- and C-lobes of CaM bind the {1-5} motif located at the ends of the target in a structurally identical manner. Methionine residues at positions 51 (corresponding to 124 in the C-lobe), 71 (144), and 72 (145) of the CaM amino acid sequence are key hydrophobic residues for this interaction. They are located at the N- and C-boundaries of the even EF-hand motifs. The hydrophobic core of CaM ('Ф-quatrefoil') consists of 10 amino acids in the N-lobe (and in the C-lobe): Phe
Language	English
Publishing date	2022-09-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2123391
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Article ; Online: System Approach for Building of Calcium-Binding Sites in Proteins.

Denesyuk, Alexander I / Permyakov, Sergei E / Johnson, Mark S / Denessiouk, Konstantin / Permyakov, Eugene A

Biomolecules

2020 Volume 10, Issue 4

Abstract: We introduce five new local metal cation (first of all, ... ...

Abstract	We introduce five new local metal cation (first of all, Ca
MeSH term(s)	Binding Sites ; Calcium/metabolism ; Cations ; Models, Molecular ; Proteins/chemistry ; Proteins/metabolism
Chemical Substances	Cations ; Proteins ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2020-04-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom10040588
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Article ; Online: NBCZone: Universal three-dimensional construction of eleven amino acids near the catalytic nucleophile and base in the superfamily of (chymo)trypsin-like serine fold proteases.

Denesyuk, Alexander I / Johnson, Mark S / Salo-Ahen, Outi M H / Uversky, Vladimir N / Denessiouk, Konstantin

International journal of biological macromolecules

2020 Volume 153, Page(s) 399–411

Abstract: Chymo)trypsin-like serine fold proteases belong to the serine/cysteine proteases found in eukaryotes, prokaryotes, and viruses. Their catalytic activity is carried out using a triad of amino acids, a nucleophile, a base, and an acid. For this ... ...

Abstract	(Chymo)trypsin-like serine fold proteases belong to the serine/cysteine proteases found in eukaryotes, prokaryotes, and viruses. Their catalytic activity is carried out using a triad of amino acids, a nucleophile, a base, and an acid. For this superfamily of proteases, we propose the existence of a universal 3D structure comprising 11 amino acids near the catalytic nucleophile and base - Nucleophile-Base Catalytic Zone (NBCZone). The comparison of NBCZones among 169 eukaryotic, prokaryotic, and viral (chymo)trypsin-like proteases suggested the existence of 15 distinct groups determined by the combination of amino acids located at two "key" structure-functional positions 54
MeSH term(s)	Amino Acids/chemistry ; Amino Acids/genetics ; Binding Sites ; Models, Molecular ; Protein Conformation ; Serine Endopeptidases/chemistry ; Serine Endopeptidases/genetics
Chemical Substances	Amino Acids ; trypsin-like serine protease ; Serine Endopeptidases (EC 3.4.21.-)
Keywords	covid19
Language	English
Publishing date	2020-03-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2020.03.025
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Article ; Online: Structural and functional significance of the amino acid differences Val

Denesyuk, Alexander I / Permyakov, Eugene A / Johnson, Mark S / Permyakov, Sergei E / Denessiouk, Konstantin / Uversky, Vladimir N

International journal of biological macromolecules

2021 Volume 193, Issue Pt B, Page(s) 2113–2120

Abstract: Three dimensional structures of (chymo)trypsin-like proteinase ( ... ...

Abstract	Three dimensional structures of (chymo)trypsin-like proteinase (3CL
MeSH term(s)	Amino Acid Substitution ; Coronavirus 3C Proteases/chemistry ; Coronavirus 3C Proteases/genetics ; Humans ; Mutation, Missense ; Protein Domains ; Severe acute respiratory syndrome-related coronavirus/enzymology ; Severe acute respiratory syndrome-related coronavirus/genetics ; SARS-CoV-2/enzymology ; SARS-CoV-2/genetics ; Species Specificity ; Structure-Activity Relationship
Chemical Substances	3C-like protease, SARS coronavirus (EC 3.4.22.-) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2021-11-11
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2021.11.043
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Article ; Online: The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements.

Denesyuk, Alexander / Dimitriou, Polytimi S / Johnson, Mark S / Nakayama, Toru / Denessiouk, Konstantin

PloS one

2020 Volume 15, Issue 2, Page(s) e0229376

Abstract: The alpha/beta-Hydrolases (ABH) are a structural class of proteins that are found widespread in nature and includes enzymes that can catalyze various reactions in different substrates. The catalytic versatility of the ABH fold enzymes, which has been a ... ...

Abstract	The alpha/beta-Hydrolases (ABH) are a structural class of proteins that are found widespread in nature and includes enzymes that can catalyze various reactions in different substrates. The catalytic versatility of the ABH fold enzymes, which has been a valuable property in protein engineering applications, is based on a similar acid-base-nucleophile catalytic mechanism. In our research, we are concerned with the structure that surrounds the key units of the catalytic machinery, and we have previously found conserved structural organizations that coordinate the catalytic acid, the catalytic nucleophile and the residues of the oxyanion hole. Here, we explore the architecture that surrounds the catalytic histidine at the active sites of enzymes from 40 ABH fold families, where we have identified six conserved interactions that coordinate the catalytic histidine next to the catalytic acid and the catalytic nucleophile. Specifically, the catalytic nucleophile is coordinated next to the catalytic histidine by two weak hydrogen bonds, while the catalytic acid is directly involved in the coordination of the catalytic histidine through by two weak hydrogen bonds. The imidazole ring of the catalytic histidine is coordinated by a CH-π contact and a hydrophobic interaction. Moreover, the catalytic triad residues are connected with a residue that is located at the core of the active site of ABH fold, which is suggested to be the fourth member of a "structural catalytic tetrad". Besides their role in the stability of the catalytic mechanism, the conserved elements of the catalytic site are actively involved in ligand binding and affect other properties of the catalytic activity, such as substrate specificity, enantioselectivity, pH optimum and thermostability of ABH fold enzymes. These properties are regularly targeted in protein engineering applications, and thus, the identified conserved structural elements can serve as potential modification sites in order to develop ABH fold enzymes with altered activities.
MeSH term(s)	Binding Sites ; Catalysis ; Catalytic Domain ; Histidine/chemistry ; Histidine/metabolism ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrolases/chemistry ; Hydrolases/metabolism ; Models, Molecular ; Substrate Specificity
Chemical Substances	Histidine (4QD397987E) ; Hydrolases (EC 3.-)
Language	English
Publishing date	2020-02-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0229376
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Article ; Online: Top surface blade residues and the central channel water molecules are conserved in every repeat of the integrin-like β-propeller structures.

Denesyuk, Alexander / Denessiouk, Konstantin / Johnson, Mark S

Journal of structural biology

2017 Volume 201, Issue 2, Page(s) 155–161

Abstract: An integrin-like β-propeller domain contains seven repeats of a four-stranded antiparallel β-sheet motif (blades). Previously we described a 3D structural motif within each blade of the integrin-type β-propeller. Here, we show unique structural links ... ...

Abstract	An integrin-like β-propeller domain contains seven repeats of a four-stranded antiparallel β-sheet motif (blades). Previously we described a 3D structural motif within each blade of the integrin-type β-propeller. Here, we show unique structural links that join different blades of the β-propeller structure, which together with the structural motif for a single blade are repeated in a β-propeller to provide the functional top face of the barrel, found to be involved in protein-protein interactions and substrate recognition. We compare functional top face diagrams of the integrin-type β-propeller domain and two non-integrin type β-propeller domains of virginiamycin B lyase and WD Repeat-Containing Protein 5.
MeSH term(s)	Histone-Lysine N-Methyltransferase/chemistry ; Histone-Lysine N-Methyltransferase/metabolism ; Integrins/chemistry ; Integrins/metabolism ; Lyases/chemistry ; Lyases/metabolism ; Models, Molecular ; Platelet Glycoprotein GPIIb-IIIa Complex/chemistry ; Platelet Glycoprotein GPIIb-IIIa Complex/genetics ; Platelet Glycoprotein GPIIb-IIIa Complex/metabolism ; Protein Conformation ; Protein Interaction Domains and Motifs ; Water/chemistry
Chemical Substances	Integrins ; Platelet Glycoprotein GPIIb-IIIa Complex ; WDR5 protein, human ; Water (059QF0KO0R) ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; Lyases (EC 4.-)
Language	English
Publishing date	2017-10-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2017.10.005
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Article ; Online: Structural leitmotif and functional variations of the structural catalytic core in (chymo)trypsin-like serine/cysteine fold proteinases.

Denesyuk, Alexander I / Permyakov, Sergei E / Johnson, Mark S / Permyakov, Eugene A / Uversky, Vladimir N / Denessiouk, Konstantin

International journal of biological macromolecules

2021 Volume 179, Page(s) 601–609

Abstract: ... Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411 ...

Abstract	Proteinases with the (chymo)trypsin-like serine/cysteine fold comprise a large superfamily performing their function through the Acid - Base - Nucleophile catalytic triad. In our previous work (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411), we described a universal three-dimensional (3D) structural motif, NBCZone, that contains eleven amino acids: dipeptide 42 T-43 T, pentapeptide 54 T-55 T-56 T-57 T(base)-58 T, tripeptide 195 T(nucleophile)-196 T-197 T and residue 213 T (T - numeration of amino acids in trypsin). The comparison of the NBCZones among the members of the (chymo)trypsin-like protease family suggested the existence of 15 distinct groups. Within each group, the NBCZones incorporate an identical set of conserved interactions and bonds. In the present work, the structural environment of the catalytic acid at the position 102 T and the fourth member of the "catalytic tetrad" at the position 214 T was analyzed in 169 3D structures of proteinases with the (chymo)trypsin-like serine/cysteine fold. We have identified a complete Structural Catalytic Core (SCC) consisting of two classes and four groups. The proteinases belonging to different classes and groups differ from each other by the nature of the interaction between their N- and C-terminal β-barrels. Comparative analysis of the 3CLpro(s) from SARS-CoV-2 and SARS-CoV, used as an example, showed that the amino acids at positions 103 T and 179 T affect the nature of the interaction of the "catalytic acid" core (102 T-Core, N-terminal β-barrel) with the "supplementary" core (S-Core, C-terminal β-barrel), which ultimately results in the modulation of the enzymatic activity. The reported analysis represents an important standalone contribution to the analysis and systematization of the 3D structures of (chymo)trypsin-like serine/cysteine fold proteinases. The use of the developed approach for the comparison of 3D structures will allow, in the event of the appearance of new representatives of a given fold in the PDB, to quickly determine their structural homologues with the identification of possible differences.
MeSH term(s)	Amino Acid Sequence ; Binding Sites ; COVID-19/metabolism ; Catalysis ; Catalytic Domain ; Cysteine Proteases/chemistry ; Cysteine Proteases/metabolism ; Humans ; Models, Molecular ; SARS Virus/chemistry ; SARS Virus/metabolism ; SARS-CoV-2/chemistry ; SARS-CoV-2/metabolism ; Serine Endopeptidases/chemistry ; Serine Endopeptidases/metabolism ; Serine Proteases/chemistry ; Serine Proteases/metabolism ; Trypsin/metabolism
Chemical Substances	trypsin-like serine protease ; Cysteine Proteases (EC 3.4.-) ; Serine Proteases (EC 3.4.-) ; Serine Endopeptidases (EC 3.4.21.-) ; Trypsin (EC 3.4.21.4)
Language	English
Publishing date	2021-03-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2021.03.042
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Article: Papain-like cysteine proteinase zone (PCP-zone) and PCP structural catalytic core (PCP-SCC) of enzymes with cysteine proteinase fold

Denessiouk, Konstantin / Uversky, Vladimir N / Permyakov, Sergei E / Permyakov, Eugene A / Johnson, Mark S / Denesyuk, Alexander I

International journal of biological macromolecules. 2020 Dec. 15, v. 165

2020

Abstract: ... 3CLpro presented in our earlier article (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K ...

Abstract	There are several families of cysteine proteinases with different folds – for example the (chymo)trypsin fold family and papain-like fold family – but in both families the hydrolase activity of cysteine proteinases requires a cysteine residue as the catalytic nucleophile. In this work, we have analyzed the topology of the active site regions in 146 three-dimensional structures of proteins belonging to the Papain-like Cysteine Proteinase (PCP) superfamily, which includes papain as a typical representative of this protein superfamily. All analyzed enzymes contain a unique structurally closed conformation – a “PCP-Zone” – which can be divided into two groups, Class A and Class B. Eight structurally conserved amino acids of the PCP-Zone form a common Structural Core. The Structural Core, catalytic nucleophile, catalytic base and residue Xaa – which stabilizes the side-chain conformation of the catalytic base – make up a PCP Structural Catalytic Core (PCP-SCC). The PCP-SCC of Class A and Class B are divided into 5 and 2 types, respectively. Seven variants of the mutual arrangement of the amino-acid side chains of the catalytic triad – nucleophile, base and residue Xaa – within the same fold clearly demonstrate how enzymes with the papain-like fold adapt to the need to perform diverse functions in spite of their limited structural diversity. The roles of both the PCP-Zone of SARS-CoV-2-PLpro described in this study and the NBCZone of SARS-CoV-2-3CLpro presented in our earlier article (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411) that are in contacts with inhibitors are discussed.
Keywords	Lewis bases ; active sites ; cysteine ; papain ; topology ; trypsin
Language	English
Dates of publication	2020-1215
Size	p. 1438-1446.
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2020.10.022
Database	NAL-Catalogue (AGRICOLA)

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