SMTL ID : 4fmi.6 (5 other biounits)

Merkel cell polyomavirus VP1 in complex with 3'-sialyllactosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-10-mer

Ligands

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

GAL-SIA.1: 7 residues within 4Å: Chain J: W.45, Y.50, D.51, D.114, K.264, S.266, K.268 9 PLIP interactions: 9 interactions with chain J Water bridges: J:D.114, J:S.266, J:D.114, J:S.266, J:K.268, J:K.268 Hydrophobic interactions: J:Y.50 Hydrogen bonds: J:D.51, J:K.264, J:S.266 Salt bridges: J:K.268

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: N.131, H.133, S.215, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.215, A:S.215, A:Q.217, A:P.223, A:V.225 GOL.4: 7 residues within 4Å: Chain B: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.217, B:P.223, B:V.225 Water bridges: B:Q.217 GOL.6: 8 residues within 4Å: Chain C: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.131, C:S.215, C:Q.217, C:V.225 Water bridges: C:Q.217 GOL.8: 9 residues within 4Å: Chain D: N.131, H.133, S.215, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.9 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.133, D:S.215, D:Q.217, D:P.223, D: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 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:H.133, E:S.215, E:Q.217, E:P.223, E:V.225 GOL.12: 8 residues within 4Å: Chain F: N.131, H.133, S.215, Q.217, P.223, T.224, V.225 Ligands: CL.13 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.215, F:Q.217, F:P.223, F:V.225 Water bridges: F:Q.217 GOL.14: 8 residues within 4Å: Chain G: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.15 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:H.133, G:Q.217, G:P.223, G:V.225 GOL.16: 6 residues within 4Å: Chain H: N.44, W.45, Y.112, W.113 Chain I: D.150, Q.152 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:Q.152, H:N.44, H:Y.112 Water bridges: I:Q.179 GOL.17: 9 residues within 4Å: Chain H: N.131, H.133, S.215, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.18 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:H.133, H:S.215, H:Q.217, H:P.223, H:V.225 Water bridges: H:Q.217 GOL.19: 3 residues within 4Å: Chain I: K.55, G.56, S.57 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:S.57 Water bridges: I:K.55, I:K.55 GOL.22: 8 residues within 4Å: Chain J: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.23 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:H.133, J:S.215, J:Q.217, J:P.223, J:V.225 Water bridges: J:Q.217

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

CL.3: 6 residues within 4Å: Chain A: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.2 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain B: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.4 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain C: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.6 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain D: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.8 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.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.15: 6 residues within 4Å: Chain G: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.14 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain H: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.17 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain I: N.131, H.133, S.215, I.216, Q.217 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain H: W.113 Chain I: S.58 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain J: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.22 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
F

B
G

C
H

D
I

E
J

F
P

G
Q

H
R

I
S

J
T

VP1

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