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

Merkel Cell Polyomavirus VP1 in complex with Disialyllactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 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 C: W.45, Y.50, D.51, D.114, K.264, S.266, K.268 6 PLIP interactions: 6 interactions with chain C Water bridges: C:D.114, C:D.114, C:D.114, C:D.114, C:D.114, C:D.114, C:S.266 Hydrophobic interactions: C:Y.50 Hydrogen bonds: C:D.51, C:K.264, C:S.266 Salt bridges: C:K.268 GAL-SIA.2: 7 residues within 4Å: Chain G: W.45, Y.50, D.51, D.114, K.264, S.266, K.268 8 PLIP interactions: 8 interactions with chain G Water bridges: G:D.114, G:D.114, G:D.114, G:D.114, G:D.114, G:D.114, G:D.114, G:S.266, G:K.268 Hydrophobic interactions: G:Y.50 Hydrogen bonds: G:D.51, G:K.264, G:S.266 Salt bridges: G:K.268 GAL-SIA.3: 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:D.114, J:D.114, J:D.114, 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

27 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.6 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: K.116, R.117, V.118, H.119, D.120 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain B: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.9 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain B: K.116, R.117, V.118, H.119, D.120 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain C: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.12 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain C: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain D: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.15 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain D: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain E: N.131, H.133, S.215, Q.217, P.223, T.224, V.225 Ligands: CL.18 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain E: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain F: N.131, H.133, S.215, Q.217, P.223, T.224, V.225 Ligands: CL.22 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain F: E.208, N.209, R.211, D.238, V.242, G.243, P.244, L.245 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain F: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain G: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.26 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain G: E.208, N.209, R.211, D.238, G.243, P.244, L.245 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain G: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain H: N.44, W.45, Y.112, W.113 Chain I: D.150, Q.152 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain H: N.131, H.133, S.215, Q.217, P.223, T.224, V.225 Ligands: CL.31 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain H: E.208, N.209, R.211, D.238, V.242, G.243, P.244, L.245 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain H: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain I: N.44, W.45, Y.112, W.113 Chain J: D.150, Y.151, Q.152, Q.179 Ligand excluded by PLIP GOL.33: 8 residues within 4Å: Chain I: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.37 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain I: E.208, N.209, R.211, D.238, G.243, P.244, L.245 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain I: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain I: K.55, G.56, S.57 Ligand excluded by PLIP GOL.38: 9 residues within 4Å: Chain J: N.131, H.133, S.215, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.40 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain J: K.116, R.117, H.119, D.120 Ligand excluded by PLIP

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

CL.6: 6 residues within 4Å: Chain A: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.4 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.7 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain C: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.10 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.18: 6 residues within 4Å: Chain E: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.16 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain F: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.19 Ligand excluded by PLIP CL.26: 6 residues within 4Å: Chain G: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.23 Ligand excluded by PLIP CL.31: 6 residues within 4Å: Chain H: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.28 Ligand excluded by PLIP CL.37: 6 residues within 4Å: Chain I: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.33 Ligand excluded by PLIP CL.40: 6 residues within 4Å: Chain J: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.38 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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