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

Merkel Cell Polyomavirus VP1 in complex with Disialyllactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-pentamer

Ligands

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-functional Binders)

GAL-SIA.1: 7 residues within 4Å: Chain B: W.45, Y.50, D.51, D.114, K.264, S.266, K.268 6 PLIP interactions: 6 interactions with chain B Water bridges: B:D.114, B:D.114, B:D.114, B:D.114, B:S.266, B:S.266 Hydrophobic interactions: B:Y.50 Hydrogen bonds: B:D.51, B:K.264, B:S.266 Salt bridges: B:K.268

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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:S.58 GOL.3: 8 residues within 4Å: Chain A: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.217, A:P.223, A:V.225 Water bridges: A:Q.217, A:V.225 GOL.4: 4 residues within 4Å: Chain A: K.116, R.117, H.119, D.120 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.116, A:R.117, A:D.120, A:D.120 GOL.6: 8 residues within 4Å: Chain B: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.131, B:S.215, B:Q.217, B:V.225 Water bridges: B:V.225 GOL.7: 4 residues within 4Å: Chain B: K.116, R.117, H.119, D.120 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.117, B:R.117, B:D.120 Water bridges: B:D.120 GOL.9: 7 residues within 4Å: Chain C: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.217, C:P.223, C:V.225 Water bridges: C:Q.217 GOL.10: 4 residues within 4Å: Chain C: K.116, R.117, H.119, D.120 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.116, C:R.117 Water bridges: C:R.117, C:D.120 GOL.12: 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.13: 7 residues within 4Å: Chain D: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.15 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.217, D:P.223, D:V.225 Water bridges: D:Q.217, D:V.225 GOL.14: 4 residues within 4Å: Chain D: K.116, R.117, H.119, D.120 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.116, D:R.117, D:D.120 Water bridges: D:K.116, D:D.120, D:D.120 GOL.16: 7 residues within 4Å: Chain E: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.19 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.131, E:Q.217, E:V.225 Water bridges: E:Q.217 GOL.17: 7 residues within 4Å: Chain E: E.208, N.209, R.211, D.238, G.243, P.244, L.245 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.211, E:R.211, E:D.238 GOL.18: 4 residues within 4Å: Chain E: K.116, R.117, H.119, D.120 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:K.116, E:R.117, E:H.119 Water bridges: E:R.117, E:D.120, E:Y.121

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

CL.5: 6 residues within 4Å: Chain A: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.3 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.6 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain C: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.9 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain D: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.13 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain E: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.16 Ligand excluded by PLIP

Links

RCSB   PDBe   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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