SMTL ID : 1sie.3 (4 other biounits)

MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.65 Å

Oligo State

homo-36-mer

Ligands

36 x NAG- GAL- SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA-SIA.1: 9 residues within 4Å: Chain A: Y.72, R.77, G.78, S.89, N.93, K.186, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.78, A:N.93, A:N.93, A:S.89 Salt bridges: A:K.186 NAG-GAL-SIA-SIA.2: 8 residues within 4Å: Chain B: Y.72, R.77, G.78, I.79, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.78, B:N.93, B:S.89 NAG-GAL-SIA-SIA.3: 8 residues within 4Å: Chain C: Y.72, R.77, G.78, I.79, N.93, T.291, H.298 Chain D: D.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.79 NAG-GAL-SIA-SIA.4: 7 residues within 4Å: Chain D: Y.72, R.77, G.78, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.93 Salt bridges: D:K.186 NAG-GAL-SIA-SIA.5: 11 residues within 4Å: Chain A: D.85 Chain E: Y.72, R.77, G.78, I.79, S.89, N.93, T.291, N.293, V.296, H.298 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.79, E:N.93, E:S.89 Salt bridges: E:K.186 NAG-GAL-SIA-SIA.6: 10 residues within 4Å: Chain F: Y.72, R.77, G.78, I.79, E.87, S.89, N.93, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:I.79, F:N.93, F:N.93, F:S.89 Salt bridges: F:K.186 NAG-GAL-SIA-SIA.7: 9 residues within 4Å: Chain G: Y.72, R.77, G.78, S.89, N.93, K.186, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.78, G:N.93, G:N.93, G:S.89 Salt bridges: G:K.186 NAG-GAL-SIA-SIA.8: 8 residues within 4Å: Chain H: Y.72, R.77, G.78, I.79, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.78, H:N.93, H:S.89 NAG-GAL-SIA-SIA.9: 8 residues within 4Å: Chain I: Y.72, R.77, G.78, I.79, N.93, T.291, H.298 Chain J: D.85 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:I.79 NAG-GAL-SIA-SIA.10: 7 residues within 4Å: Chain J: Y.72, R.77, G.78, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.93 Salt bridges: J:K.186 NAG-GAL-SIA-SIA.11: 11 residues within 4Å: Chain G: D.85 Chain K: Y.72, R.77, G.78, I.79, S.89, N.93, T.291, N.293, V.296, H.298 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:I.79, K:N.93, K:S.89 Salt bridges: K:K.186 NAG-GAL-SIA-SIA.12: 10 residues within 4Å: Chain L: Y.72, R.77, G.78, I.79, E.87, S.89, N.93, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:I.79, L:N.93, L:N.93, L:S.89 Salt bridges: L:K.186 NAG-GAL-SIA-SIA.13: 9 residues within 4Å: Chain M: Y.72, R.77, G.78, S.89, N.93, K.186, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:G.78, M:N.93, M:N.93, M:S.89 Salt bridges: M:K.186 NAG-GAL-SIA-SIA.14: 8 residues within 4Å: Chain N: Y.72, R.77, G.78, I.79, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:G.78, N:N.93, N:S.89 NAG-GAL-SIA-SIA.15: 8 residues within 4Å: Chain O: Y.72, R.77, G.78, I.79, N.93, T.291, H.298 Chain P: D.85 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:I.79 NAG-GAL-SIA-SIA.16: 7 residues within 4Å: Chain P: Y.72, R.77, G.78, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.93 Salt bridges: P:K.186 NAG-GAL-SIA-SIA.17: 11 residues within 4Å: Chain M: D.85 Chain Q: Y.72, R.77, G.78, I.79, S.89, N.93, T.291, N.293, V.296, H.298 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:I.79, Q:N.93, Q:S.89 Salt bridges: Q:K.186 NAG-GAL-SIA-SIA.18: 10 residues within 4Å: Chain R: Y.72, R.77, G.78, I.79, E.87, S.89, N.93, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:I.79, R:N.93, R:N.93, R:S.89 Salt bridges: R:K.186 NAG-GAL-SIA-SIA.19: 9 residues within 4Å: Chain S: Y.72, R.77, G.78, S.89, N.93, K.186, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain S Hydrogen bonds: S:G.78, S:N.93, S:N.93, S:S.89 Salt bridges: S:K.186 NAG-GAL-SIA-SIA.20: 8 residues within 4Å: Chain T: Y.72, R.77, G.78, I.79, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:G.78, T:N.93, T:S.89 NAG-GAL-SIA-SIA.21: 8 residues within 4Å: Chain U: Y.72, R.77, G.78, I.79, N.93, T.291, H.298 Chain V: D.85 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:I.79 NAG-GAL-SIA-SIA.22: 7 residues within 4Å: Chain V: Y.72, R.77, G.78, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:N.93 Salt bridges: V:K.186 NAG-GAL-SIA-SIA.23: 11 residues within 4Å: Chain S: D.85 Chain W: Y.72, R.77, G.78, I.79, S.89, N.93, T.291, N.293, V.296, H.298 2 PLIP interactions: 2 interactions with chain W Hydrogen bonds: W:I.79, W:N.93, W:S.89 Salt bridges: W:K.186 NAG-GAL-SIA-SIA.24: 10 residues within 4Å: Chain X: Y.72, R.77, G.78, I.79, E.87, S.89, N.93, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain X Hydrogen bonds: X:I.79, X:N.93, X:N.93, X:S.89 Salt bridges: X:K.186 NAG-GAL-SIA-SIA.25: 9 residues within 4Å: Chain Y: Y.72, R.77, G.78, S.89, N.93, K.186, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain Y Hydrogen bonds: Y:G.78, Y:N.93, Y:N.93, Y:S.89 Salt bridges: Y:K.186 NAG-GAL-SIA-SIA.26: 8 residues within 4Å: Chain Z: Y.72, R.77, G.78, I.79, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain Z Hydrogen bonds: Z:G.78, Z:N.93, Z:S.89 NAG-GAL-SIA-SIA.27: 8 residues within 4Å: Chain 0: Y.72, R.77, G.78, I.79, N.93, T.291, H.298 Chain 1: D.85 1 PLIP interactions: 1 interactions with chain 0 Hydrogen bonds: 0:I.79 NAG-GAL-SIA-SIA.28: 7 residues within 4Å: Chain 1: Y.72, R.77, G.78, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain 1 Hydrogen bonds: 1:N.93 Salt bridges: 1:K.186 NAG-GAL-SIA-SIA.29: 11 residues within 4Å: Chain 2: Y.72, R.77, G.78, I.79, S.89, N.93, T.291, N.293, V.296, H.298 Chain Y: D.85 2 PLIP interactions: 2 interactions with chain 2 Hydrogen bonds: 2:I.79, 2:N.93, 2:S.89 Salt bridges: 2:K.186 NAG-GAL-SIA-SIA.30: 10 residues within 4Å: Chain 3: Y.72, R.77, G.78, I.79, E.87, S.89, N.93, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain 3 Hydrogen bonds: 3:I.79, 3:N.93, 3:N.93, 3:S.89 Salt bridges: 3:K.186 NAG-GAL-SIA-SIA.31: 9 residues within 4Å: Chain 4: Y.72, R.77, G.78, S.89, N.93, K.186, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain 4 Hydrogen bonds: 4:G.78, 4:N.93, 4:N.93, 4:S.89 Salt bridges: 4:K.186 NAG-GAL-SIA-SIA.32: 8 residues within 4Å: Chain 5: Y.72, R.77, G.78, I.79, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain 5 Hydrogen bonds: 5:G.78, 5:N.93, 5:S.89 NAG-GAL-SIA-SIA.33: 8 residues within 4Å: Chain 6: Y.72, R.77, G.78, I.79, N.93, T.291, H.298 Chain 7: D.85 1 PLIP interactions: 1 interactions with chain 6 Hydrogen bonds: 6:I.79 NAG-GAL-SIA-SIA.34: 7 residues within 4Å: Chain 7: Y.72, R.77, G.78, N.93, T.291, V.296, H.298 1 PLIP interactions: 1 interactions with chain 7 Hydrogen bonds: 7:N.93 Salt bridges: 7:K.186 NAG-GAL-SIA-SIA.35: 11 residues within 4Å: Chain 4: D.85 Chain 8: Y.72, R.77, G.78, I.79, S.89, N.93, T.291, N.293, V.296, H.298 2 PLIP interactions: 2 interactions with chain 8 Hydrogen bonds: 8:I.79, 8:N.93, 8:S.89 Salt bridges: 8:K.186 NAG-GAL-SIA-SIA.36: 10 residues within 4Å: Chain 9: Y.72, R.77, G.78, I.79, E.87, S.89, N.93, T.291, V.296, H.298 2 PLIP interactions: 2 interactions with chain 9 Hydrogen bonds: 9:I.79, 9:N.93, 9:N.93, 9:S.89 Salt bridges: 9:K.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stehle, T. et al., Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments. Structure (1996)

Release Date

1996-06-20

Peptides

POLYOMAVIRUS COAT PROTEIN VP1: ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

M
A

N
B

O
C

P
D

Q
E

R
F

S
A

T
B

U
C

V
D

W
E

X
F

Y
A

Z
B

0
C

1
D

2
E

3
F

4
A

5
B

6
C

7
D

8
E

9
F

POLYOMAVIRUS COAT PROTEIN VP1

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