SMTL ID : 5cpx.1

Crystal structure of murine polyomavirus PTA strain VP1 in complex with the DSLNT glycan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-pentamer

Ligands

3 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)(Non-covalent)

NAG-GAL-SIA.1: 10 residues within 4Å: Chain A: Y.40, R.45, G.46, E.59, N.61, T.62, T.259, N.261, H.266 Chain B: D.53 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.61, A:N.61, A:Y.40, A:Y.40, A:R.45, A:G.46, A:H.266 Water bridges: A:I.47, A:E.59, A:Q.39, A:N.261, A:N.261, A:N.261 Salt bridges: A:R.45, A:H.266 NAG-GAL-SIA.4: 10 residues within 4Å: Chain D: Y.40, R.45, G.46, E.59, N.61, T.62, T.259, N.261, H.266 Chain E: D.53 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.61, D:N.61, D:Y.40, D:R.45, D:G.46, D:H.266 Water bridges: D:I.47, D:Y.40, D:Y.40, D:N.261, D:N.261 Salt bridges: D:R.45, D:H.266 NAG-GAL-SIA.5: 10 residues within 4Å: Chain A: D.53 Chain E: Y.40, R.45, G.46, E.59, N.61, T.62, T.259, N.261, H.266 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.61, E:N.61, E:Y.40, E:Y.40, E:R.45, E:G.46, E:N.261, E:H.266 Water bridges: E:I.47, E:E.59 Salt bridges: E:R.45, E:H.266 Hydrophobic interactions: A:D.53

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

GAL-SIA.2: 10 residues within 4Å: Chain B: Y.40, R.45, G.46, E.59, N.61, T.62, T.259, N.261, H.266 Chain C: D.53 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.61, B:N.61, B:Y.40, B:Y.40, B:R.45, B:G.46, B:N.261, B:H.266 Water bridges: B:I.47, B:Q.39, B:R.257 Salt bridges: B:R.45, B:H.266 Hydrophobic interactions: C:D.53 GAL-SIA.3: 10 residues within 4Å: Chain C: Y.40, R.45, G.46, E.59, N.61, T.62, T.259, N.261, H.266 Chain D: D.53 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.46, C:N.61, C:N.61, C:Y.40, C:R.45, C:G.46, C:H.266 Water bridges: C:Y.40, C:Y.40, C:N.261, C:N.261, C:N.261 Salt bridges: C:R.45, C:H.266 Hydrophobic interactions: D:D.53

4 x GOL: GLYCEROL(Non-covalent)

GOL.6: 8 residues within 4Å: Chain A: E.203, N.204, R.206, D.233, V.237, G.238, P.239, L.240 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.204, A:R.206, A:R.206, A:D.233, A:D.233, A:L.240 GOL.7: 3 residues within 4Å: Chain B: K.154, E.155, E.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.155, B:E.156, B:E.156 GOL.8: 3 residues within 4Å: Chain D: K.154, E.155, E.156 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.155, D:E.156 Water bridges: D:E.156 GOL.9: 8 residues within 4Å: Chain E: E.203, N.204, R.206, D.233, V.237, G.238, P.239, L.240 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.204, E:R.206, E:R.206, E:D.233, E:L.240

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Buch, M.H. et al., Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity. Plos Pathog. (2015)

Release Date

2015-10-28

Peptides

VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

VP1

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