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

Structure of unliganded B-Lymphotropic Polyomavirus VP1

Coordinates

PDB Format

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.8, H2O.9 CA.5: 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.16, H2O.24 CA.8: 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.24, H2O.32 CA.10: 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.31, H2O.39 CA.13: 3 residues within 4Å: Chain A: S.191, E.194 Chain E: E.23 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: E:E.23, A:S.191, H2O.9, H2O.9, H2O.38

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

EDO.2: 8 residues within 4Å: Chain A: E.194, N.195, R.197, D.224, V.228, G.229, P.230, L.231 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.197, A:R.197, A:D.224, A:V.228 Water bridges: A:N.195 EDO.3: 8 residues within 4Å: Chain A: Q.21, S.91, V.92, K.93, T.219, N.265, V.266, T.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.21, A:T.219, A:N.265 Water bridges: A:T.219 EDO.4: 2 residues within 4Å: Chain A: A.24, Y.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.25, A:Y.25 EDO.6: 7 residues within 4Å: Chain B: E.194, N.195, R.197, D.224, G.229, P.230, L.231 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.197, B:R.197, B:V.228 Water bridges: B:N.195 EDO.7: 6 residues within 4Å: Chain B: T.126, H.128, P.210, V.211, M.212, A.245 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.128, B:V.211 Water bridges: B:T.126, B:T.126, B:T.203, B:T.203 EDO.9: 4 residues within 4Å: Chain C: V.96, H.128, M.212, Q.213 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.128, C:Q.213 EDO.11: 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:Q.21, D:T.219, D:T.219, D:T.267 EDO.12: 7 residues within 4Å: Chain D: K.93, N.216 Chain E: N.193, E.194, R.197, D.224, E.225 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:K.93, D:N.216, E:N.193 Water bridges: E:D.224 EDO.14: 8 residues within 4Å: Chain E: Q.21, S.91, V.92, K.93, T.219, N.265, V.266, T.267 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.21, E:S.91, E:N.265 Water bridges: E:T.219 EDO.15: 5 residues within 4Å: Chain D: E.8, L.10 Chain E: N.226, G.227, R.271 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:N.226, E:R.271, D:E.8 EDO.16: 8 residues within 4Å: Chain A: N.193, E.194, R.197, D.224, E.225 Chain E: K.93, N.216, S.217 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:K.93, A:E.194, A:R.197 Water bridges: E:N.216, A:R.197, A:R.197 EDO.17: 4 residues within 4Å: Chain E: V.96, H.128, M.212, Q.213 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.213 EDO.18: 7 residues within 4Å: Chain E: E.194, N.195, R.197, D.224, V.228, G.229, P.230 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.197, E:R.197, E:D.224, E:V.228

Links

RCSB   PDBe   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
A

B
B

C
C

D
D

E
E

Major Capsid Protein VP1

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