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

3 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.217, A:P.223, A:V.225 GOL.6: 8 residues within 4Å: Chain B: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.133, B:Q.217, B:P.223, B:V.225 GOL.10: 8 residues within 4Å: Chain E: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.11 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:H.133, E:Q.217, E:P.223, E:V.225

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

CL.5: 5 residues within 4Å: Chain A: N.131, H.133, S.215, I.216 Ligands: GOL.4 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain B: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.6 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain C: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain D: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain E: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.10 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain F: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain G: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain H: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain I: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain J: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP

1 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.14: 7 residues within 4Å: Chain H: W.45, Y.50, D.51, D.114, K.264, S.266, K.268 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:Y.50 Hydrogen bonds: H:D.51, H:K.264, H:S.266 Salt bridges: H:K.268

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
P

B
Q

C
R

D
S

E
T

F
F

G
G

H
H

I
I

J
J

VP1

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