SMTL ID : 4fmj.5 (5 other biounits)

Merkel cell polyomavirus VP1 in complex with GD1a oligosaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-10-mer

Ligands

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

GAL-SIA.1: 7 residues within 4Å: Chain A: W.45, Y.50, D.51, D.114, K.264, S.266, K.268 6 PLIP interactions: 6 interactions with chain A Water bridges: A:D.114, A:D.114 Hydrophobic interactions: A:Y.50 Hydrogen bonds: A:D.51, A:K.264, A:S.266, A:K.268 Salt bridges: A:K.268 GAL-SIA.2: 7 residues within 4Å: Chain C: W.45, Y.50, D.51, D.114, K.264, S.266, K.268 8 PLIP interactions: 8 interactions with chain C Water bridges: C:D.114, C:D.114, C:D.114, C:S.266, C:S.266, C:K.268, C:K.268 Hydrophobic interactions: C:Y.50 Hydrogen bonds: C:D.51, C:K.264, C:S.266 Salt bridges: C:K.268 GAL-SIA.3: 6 residues within 4Å: Chain E: W.45, Y.50, D.51, K.264, S.266, K.268 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:Y.50 Hydrogen bonds: E:D.51, E:K.264, E:S.266, E:K.268 Water bridges: E:D.114, E:S.266 Salt bridges: E:K.268

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.133, A:Q.217, A:P.223, A:V.225 GOL.7: 8 residues within 4Å: Chain C: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.133, C:S.215, C:Q.217, C:P.223, C:V.225 GOL.9: 3 residues within 4Å: Chain D: Y.50, D.51, K.264 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.51, D:D.51, D:K.264 GOL.12: 8 residues within 4Å: Chain F: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.13 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:H.133, F:Q.217, F:P.223, F:V.225 GOL.15: 7 residues within 4Å: Chain H: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.16 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:H.133, H:Q.217, H:P.223, H:V.225

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

CL.5: 6 residues within 4Å: Chain A: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.4 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain C: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.7 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain D: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain E: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain F: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.12 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain G: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain H: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.15 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain I: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain J: N.131, H.133, S.215, I.216, Q.217 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: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

D
N

E
O

F
A

G
B

H
C

I
D

J
E

VP1

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