SMTL ID : 4fmh.5 (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

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

29 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: N.44, W.45, Y.112, W.113 Chain B: D.150, Q.152 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.8 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain B: N.131, H.133, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.11 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain B: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain C: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.14 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain C: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain D: N.44, W.45, Y.112, W.113 Chain E: D.150, Y.151, Q.152, Q.179 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain D: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.18 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain D: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain E: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.22 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain E: E.208, N.209, R.211, D.238, G.243, P.244, L.245 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain E: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain F: N.131, H.133, S.215, Q.217, P.223, T.224, V.225 Ligands: CL.25 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain F: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain F: Q.145, L.181, K.186, S.205 Chain J: E.25, Y.27 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain G: N.44, W.45, Y.112, W.113 Chain H: D.150, Q.152 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain G: 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 G: E.208, N.209, R.211, D.238, V.242, G.243, P.244, L.245 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain G: K.116, R.117, V.118, H.119, D.120 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain H: N.44, W.45, Y.112, W.113 Chain I: D.150, Y.151, Q.152, Q.179 Ligand excluded by PLIP GOL.33: 9 residues within 4Å: Chain H: N.131, H.133, S.215, Q.217, P.223, T.224, V.225, L.226 Ligands: CL.36 Ligand excluded by PLIP GOL.34: 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.35: 4 residues within 4Å: Chain H: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.37: 8 residues within 4Å: Chain I: N.131, H.133, S.215, Q.217, P.223, T.224, V.225 Ligands: CL.40 Ligand excluded by PLIP GOL.38: 4 residues within 4Å: Chain I: K.116, R.117, H.119, D.120 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain I: W.45, Y.50, D.51, K.264 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain J: N.131, H.133, Q.217, P.223, T.224, V.225 Ligands: CL.43 Ligand excluded by PLIP GOL.42: 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.8: 6 residues within 4Å: Chain A: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.6 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain B: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.9 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain C: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.12 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain D: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.16 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain E: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.19 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain F: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.23 Ligand excluded by PLIP CL.31: 6 residues within 4Å: Chain G: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.28 Ligand excluded by PLIP CL.36: 6 residues within 4Å: Chain H: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.33 Ligand excluded by PLIP CL.40: 6 residues within 4Å: Chain I: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.37 Ligand excluded by PLIP CL.43: 6 residues within 4Å: Chain J: N.131, H.133, S.215, I.216, Q.217 Ligands: GOL.41 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
A

B
B

C
C

D
D

E
E

F
K

G
L

H
M

I
N

J
O

VP1

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