SMTL ID : 4mbx.2 (1 other biounit)

Structure of unliganded B-Lymphotropic Polyomavirus VP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-pentamer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.23 Chain B: S.191, E.194 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.23, A:E.23, B:S.191, H2O.5, H2O.13 CA.6: 3 residues within 4Å: Chain B: E.23 Chain C: S.191, E.194 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:S.191, B:E.23, B:E.23, H2O.14, H2O.20 CA.12: 3 residues within 4Å: Chain C: E.23 Chain D: S.191, E.194 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.23, C:E.23, D:S.191, H2O.20, H2O.24 CA.14: 3 residues within 4Å: Chain D: E.23 Chain E: S.191, E.194 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: E:S.191, D:E.23, D:E.23, H2O.27, H2O.34 CA.17: 3 residues within 4Å: Chain A: S.191, E.194 Chain E: E.23 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: E:E.23, E:E.23, A:S.191, H2O.8, H2O.34

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: E.194, N.195, R.197, D.224, V.228, G.229, P.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.197, A:R.197, A:V.228 EDO.3: 8 residues within 4Å: Chain A: Q.21, S.91, V.92, K.93, T.219, N.265, V.266, T.267 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.21, A:T.219, A:T.267 EDO.4: 4 residues within 4Å: Chain A: L.39, N.44, S.45, V.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.45 EDO.5: 6 residues within 4Å: Chain A: K.93, N.216 Chain B: N.193, E.194, R.197, D.224 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.193, A:K.93, A:N.216 EDO.7: 8 residues within 4Å: Chain B: Q.21, S.91, V.92, K.93, T.219, N.265, V.266, T.267 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.21, B:T.219, B:N.265, B:T.267 EDO.8: 4 residues within 4Å: Chain B: V.96, H.128, M.212, Q.213 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.213 EDO.9: 7 residues within 4Å: Chain A: E.8, L.10 Chain B: E.88, G.227, V.228, R.269, R.271 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.227, B:R.269, B:R.271, B:R.271 EDO.10: 8 residues within 4Å: Chain B: E.194, N.195, R.197, D.224, V.228, G.229, P.230, L.231 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.197, B:R.197, B:V.228 EDO.11: 4 residues within 4Å: Chain B: Y.25, L.26, N.27, R.29 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.27, B:N.27 Water bridges: B:N.27, B:R.29, B:R.29 EDO.13: 6 residues within 4Å: Chain C: E.8, L.10 Chain D: N.226, G.227, V.228, R.271 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.226, D:R.271, D:R.271 EDO.15: 8 residues within 4Å: Chain D: Q.21, S.91, V.92, K.93, T.219, N.265, V.266, T.267 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.91, D:T.219, D:N.265, D:T.267 EDO.16: 7 residues within 4Å: Chain D: K.93, N.216, S.217 Chain E: N.193, E.194, R.197, D.224 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:R.197, D:K.93, D:N.216 Water bridges: E:E.225 EDO.18: 6 residues within 4Å: Chain D: E.8, L.10 Chain E: N.226, G.227, V.228, R.271 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.227, E:R.271, E:R.271, D:E.8 EDO.19: 5 residues within 4Å: Chain A: S.252, E.253 Chain E: G.114, S.115, S.116 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.114, E:S.116, E:S.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neu, U. et al., Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands. Plos Pathog. (2013)

Release Date

2013-12-04

Peptides

Major Capsid Protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

Major Capsid Protein VP1

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