SMTL ID : 4fmg.1 (5 other biounits)

Merkel Cell Polyomavirus VP1 Unassembled Pentamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-pentamer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: N.44, W.45, Y.112, W.113 Chain B: D.150, Q.152 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.152, A:N.44, A:Y.112, A:Y.112 Water bridges: B:Q.179 GOL.2: 8 residues within 4Å: Chain A: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.131, A:Q.217, A:V.225 Water bridges: A:Q.227 GOL.3: 5 residues within 4Å: Chain A: K.116, R.117, V.118, H.119, D.120 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.116, A:R.117, A:V.118, A:D.120 GOL.5: 8 residues within 4Å: Chain B: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.215, B:Q.217, B:V.225 GOL.6: 4 residues within 4Å: Chain B: K.116, R.117, H.119, D.120 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.117, B:R.117, B:D.120 Water bridges: B:R.117, B:D.120 GOL.8: 8 residues within 4Å: Chain C: N.131, H.133, S.215, Q.217, P.223, T.224, V.225 Ligands: CL.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.215, C:Q.217, C:P.223, C:V.225 Water bridges: C:Q.217 GOL.9: 4 residues within 4Å: Chain C: K.116, R.117, H.119, D.120 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.116, C:R.117 Water bridges: C:K.116, C:R.117, C:R.117, C:R.117, C:Y.121 GOL.11: 8 residues within 4Å: Chain D: N.44, W.45, Y.112, W.113 Chain E: D.150, Y.151, Q.152, Q.179 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:N.44, D:Y.112, D:W.113, E:Q.179 GOL.12: 8 residues within 4Å: Chain D: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.217, D:P.223, D:V.225 Water bridges: D:Q.217 GOL.14: 6 residues within 4Å: Chain E: N.131, Q.217, P.223, T.224, V.225 Ligands: CL.15 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.131, E:Q.217, E:V.225 Water bridges: E:S.215

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 6 residues within 4Å: Chain A: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.2 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain B: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.5 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain C: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.8 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain D: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.12 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain E: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.14 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neu, U. et al., Structures of Merkel Cell Polyomavirus VP1 Complexes Define a Sialic Acid Binding Site Required for Infection. Plos Pathog. (2012)

Release Date

2012-09-05

Peptides

VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

VP1

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