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

MURINE POLYOMAVIRUS COMPLEXED WITH 3'SIALYL LACTOSE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.65 Å

Oligo State

homo-36-mer

Ligands

36 x BGC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-SIA.1: 10 residues within 4Å: Chain A: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, V.296, H.298 Chain B: D.85 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.93, A:N.93, A:Y.72, A:Y.72, A:R.77, A:H.298 Hydrophobic interactions: A:V.296 Salt bridges: A:R.77 BGC-GAL-SIA.2: 10 residues within 4Å: Chain B: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, V.296, H.298 Chain C: D.85 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.80, B:G.78, B:G.78, B:N.93, B:Y.72, B:H.298 Hydrophobic interactions: B:V.296 Salt bridges: B:R.77 BGC-GAL-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 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.93, C:Y.72, C:R.77, C:H.298 Salt bridges: C:R.77 BGC-GAL-SIA.4: 9 residues within 4Å: Chain D: Y.72, R.77, G.78, N.80, N.93, T.291, V.296, H.298 Chain E: D.85 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.80, D:N.93, D:Y.72, D:Y.72, D:Y.72, D:R.77, D:H.298 Hydrophobic interactions: D:V.296 Salt bridges: D:R.77 BGC-GAL-SIA.5: 11 residues within 4Å: Chain A: D.85 Chain E: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, N.293, V.296, H.298 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:G.78, E:I.79, E:N.93, E:T.94, E:T.94, E:Y.72, E:Y.72, E:Y.72, E:H.298 Hydrophobic interactions: E:V.296, A:D.85 Salt bridges: E:R.77, E:H.298 BGC-GAL-SIA.6: 10 residues within 4Å: Chain F: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, N.293, V.296, H.298 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:I.79, F:N.93, F:Y.72, F:R.77, F:H.298 Hydrophobic interactions: F:V.296 Salt bridges: F:R.77 BGC-GAL-SIA.7: 10 residues within 4Å: Chain G: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, V.296, H.298 Chain H: D.85 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:N.93, G:N.93, G:Y.72, G:Y.72, G:R.77, G:H.298 Hydrophobic interactions: G:V.296 Salt bridges: G:R.77 BGC-GAL-SIA.8: 10 residues within 4Å: Chain H: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, V.296, H.298 Chain I: D.85 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:N.80, H:G.78, H:G.78, H:N.93, H:Y.72, H:H.298 Hydrophobic interactions: H:V.296 Salt bridges: H:R.77 BGC-GAL-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 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:N.93, I:Y.72, I:R.77, I:H.298 Salt bridges: I:R.77 BGC-GAL-SIA.10: 9 residues within 4Å: Chain J: Y.72, R.77, G.78, N.80, N.93, T.291, V.296, H.298 Chain K: D.85 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:N.80, J:N.93, J:Y.72, J:Y.72, J:Y.72, J:R.77, J:H.298 Hydrophobic interactions: J:V.296 Salt bridges: J:R.77 BGC-GAL-SIA.11: 11 residues within 4Å: Chain G: D.85 Chain K: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, N.293, V.296, H.298 8 PLIP interactions: 7 interactions with chain K, 1 interactions with chain G Hydrogen bonds: K:G.78, K:I.79, K:N.93, K:T.94, K:T.94, K:Y.72, K:Y.72, K:Y.72, K:H.298 Hydrophobic interactions: K:V.296, G:D.85 Salt bridges: K:R.77, K:H.298 BGC-GAL-SIA.12: 11 residues within 4Å: Chain F: D.85 Chain L: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, N.293, V.296, H.298 6 PLIP interactions: 5 interactions with chain L, 1 interactions with chain F Hydrogen bonds: L:I.79, L:N.93, L:Y.72, L:R.77, L:H.298 Hydrophobic interactions: L:V.296, F:D.85 Salt bridges: L:R.77 BGC-GAL-SIA.13: 10 residues within 4Å: Chain M: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, V.296, H.298 Chain N: D.85 6 PLIP interactions: 6 interactions with chain M Hydrogen bonds: M:N.93, M:N.93, M:Y.72, M:Y.72, M:R.77, M:H.298 Hydrophobic interactions: M:V.296 Salt bridges: M:R.77 BGC-GAL-SIA.14: 10 residues within 4Å: Chain N: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, V.296, H.298 Chain O: D.85 4 PLIP interactions: 4 interactions with chain N Hydrogen bonds: N:N.80, N:G.78, N:G.78, N:N.93, N:Y.72, N:H.298 Hydrophobic interactions: N:V.296 Salt bridges: N:R.77 BGC-GAL-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 4 PLIP interactions: 4 interactions with chain O Hydrogen bonds: O:N.93, O:Y.72, O:R.77, O:H.298 Salt bridges: O:R.77 BGC-GAL-SIA.16: 9 residues within 4Å: Chain P: Y.72, R.77, G.78, N.80, N.93, T.291, V.296, H.298 Chain Q: D.85 7 PLIP interactions: 7 interactions with chain P Hydrogen bonds: P:N.80, P:N.93, P:Y.72, P:Y.72, P:Y.72, P:R.77, P:H.298 Hydrophobic interactions: P:V.296 Salt bridges: P:R.77 BGC-GAL-SIA.17: 11 residues within 4Å: Chain M: D.85 Chain Q: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, N.293, V.296, H.298 8 PLIP interactions: 7 interactions with chain Q, 1 interactions with chain M Hydrogen bonds: Q:G.78, Q:I.79, Q:N.93, Q:T.94, Q:T.94, Q:Y.72, Q:Y.72, Q:Y.72, Q:H.298 Hydrophobic interactions: M:D.85, Q:V.296 Salt bridges: Q:R.77, Q:H.298 BGC-GAL-SIA.18: 11 residues within 4Å: Chain R: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, N.293, V.296, H.298 Chain X: D.85 6 PLIP interactions: 5 interactions with chain R, 1 interactions with chain X Hydrogen bonds: R:I.79, R:N.93, R:Y.72, R:R.77, R:H.298 Hydrophobic interactions: R:V.296, X:D.85 Salt bridges: R:R.77 BGC-GAL-SIA.19: 10 residues within 4Å: Chain S: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, V.296, H.298 Chain T: D.85 7 PLIP interactions: 7 interactions with chain S Hydrogen bonds: S:N.93, S:N.93, S:Y.72, S:Y.72, S:Y.72, S:R.77, S:H.298 Hydrophobic interactions: S:V.296 Salt bridges: S:R.77 BGC-GAL-SIA.20: 10 residues within 4Å: Chain T: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, V.296, H.298 Chain U: D.85 4 PLIP interactions: 4 interactions with chain T Hydrogen bonds: T:N.80, T:G.78, T:G.78, T:N.93, T:Y.72, T:H.298 Hydrophobic interactions: T:V.296 Salt bridges: T:R.77 BGC-GAL-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 5 PLIP interactions: 5 interactions with chain U Hydrogen bonds: U:N.93, U:Y.72, U:Y.72, U:R.77, U:H.298 Salt bridges: U:R.77 BGC-GAL-SIA.22: 9 residues within 4Å: Chain V: Y.72, R.77, G.78, N.80, N.93, T.291, V.296, H.298 Chain W: D.85 6 PLIP interactions: 6 interactions with chain V Hydrogen bonds: V:N.80, V:N.93, V:Y.72, V:Y.72, V:R.77, V:H.298 Hydrophobic interactions: V:V.296 Salt bridges: V:R.77 BGC-GAL-SIA.23: 11 residues within 4Å: Chain S: D.85 Chain W: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, N.293, V.296, H.298 8 PLIP interactions: 7 interactions with chain W, 1 interactions with chain S Hydrogen bonds: W:G.78, W:I.79, W:N.93, W:T.94, W:T.94, W:Y.72, W:Y.72, W:Y.72, W:H.298 Hydrophobic interactions: W:V.296, S:D.85 Salt bridges: W:R.77, W:H.298 BGC-GAL-SIA.24: 10 residues within 4Å: Chain X: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, N.293, V.296, H.298 5 PLIP interactions: 5 interactions with chain X Hydrogen bonds: X:I.79, X:N.93, X:Y.72, X:R.77, X:H.298 Hydrophobic interactions: X:V.296 Salt bridges: X:R.77 BGC-GAL-SIA.25: 10 residues within 4Å: Chain Y: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, V.296, H.298 Chain Z: D.85 6 PLIP interactions: 6 interactions with chain Y Hydrogen bonds: Y:N.93, Y:N.93, Y:Y.72, Y:Y.72, Y:R.77, Y:H.298 Hydrophobic interactions: Y:V.296 Salt bridges: Y:R.77 BGC-GAL-SIA.26: 10 residues within 4Å: Chain 0: D.85 Chain Z: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, V.296, H.298 4 PLIP interactions: 4 interactions with chain Z Hydrogen bonds: Z:N.80, Z:G.78, Z:G.78, Z:N.93, Z:Y.72, Z:H.298 Hydrophobic interactions: Z:V.296 Salt bridges: Z:R.77 BGC-GAL-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 4 PLIP interactions: 4 interactions with chain 0 Hydrogen bonds: 0:N.93, 0:Y.72, 0:R.77, 0:H.298 Salt bridges: 0:R.77 BGC-GAL-SIA.28: 9 residues within 4Å: Chain 1: Y.72, R.77, G.78, N.80, N.93, T.291, V.296, H.298 Chain 2: D.85 6 PLIP interactions: 6 interactions with chain 1 Hydrogen bonds: 1:N.80, 1:N.93, 1:Y.72, 1:Y.72, 1:R.77, 1:H.298 Hydrophobic interactions: 1:V.296 Salt bridges: 1:R.77 BGC-GAL-SIA.29: 11 residues within 4Å: Chain 2: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, N.293, V.296, H.298 Chain Y: D.85 8 PLIP interactions: 7 interactions with chain 2, 1 interactions with chain Y Hydrogen bonds: 2:G.78, 2:I.79, 2:N.93, 2:T.94, 2:T.94, 2:Y.72, 2:Y.72, 2:Y.72, 2:H.298 Hydrophobic interactions: 2:V.296, Y:D.85 Salt bridges: 2:R.77, 2:H.298 BGC-GAL-SIA.30: 10 residues within 4Å: Chain 3: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, N.293, V.296, H.298 5 PLIP interactions: 5 interactions with chain 3 Hydrogen bonds: 3:I.79, 3:N.93, 3:Y.72, 3:R.77, 3:H.298 Hydrophobic interactions: 3:V.296 Salt bridges: 3:R.77 BGC-GAL-SIA.31: 10 residues within 4Å: Chain 4: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, V.296, H.298 Chain 5: D.85 6 PLIP interactions: 6 interactions with chain 4 Hydrogen bonds: 4:N.93, 4:N.93, 4:Y.72, 4:Y.72, 4:R.77, 4:H.298 Hydrophobic interactions: 4:V.296 Salt bridges: 4:R.77 BGC-GAL-SIA.32: 10 residues within 4Å: Chain 5: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, V.296, H.298 Chain 6: D.85 4 PLIP interactions: 4 interactions with chain 5 Hydrogen bonds: 5:N.80, 5:G.78, 5:G.78, 5:N.93, 5:Y.72, 5:H.298 Hydrophobic interactions: 5:V.296 Salt bridges: 5:R.77 BGC-GAL-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 4 PLIP interactions: 4 interactions with chain 6 Hydrogen bonds: 6:N.93, 6:Y.72, 6:R.77, 6:H.298 Salt bridges: 6:R.77 BGC-GAL-SIA.34: 9 residues within 4Å: Chain 7: Y.72, R.77, G.78, N.80, N.93, T.291, V.296, H.298 Chain 8: D.85 7 PLIP interactions: 7 interactions with chain 7 Hydrogen bonds: 7:N.80, 7:N.93, 7:Y.72, 7:Y.72, 7:Y.72, 7:R.77, 7:H.298 Hydrophobic interactions: 7:V.296 Salt bridges: 7:R.77 BGC-GAL-SIA.35: 11 residues within 4Å: Chain 4: D.85 Chain 8: Y.72, R.77, G.78, I.79, N.93, T.94, T.291, N.293, V.296, H.298 8 PLIP interactions: 7 interactions with chain 8, 1 interactions with chain 4 Hydrogen bonds: 8:G.78, 8:I.79, 8:N.93, 8:T.94, 8:Y.72, 8:Y.72, 8:Y.72, 8:H.298 Hydrophobic interactions: 8:V.296, 4:D.85 Salt bridges: 8:R.77, 8:H.298 BGC-GAL-SIA.36: 11 residues within 4Å: Chain 3: D.85 Chain 9: Y.72, R.77, G.78, I.79, N.80, N.93, T.291, N.293, V.296, H.298 6 PLIP interactions: 5 interactions with chain 9, 1 interactions with chain 3 Hydrogen bonds: 9:I.79, 9:N.93, 9:Y.72, 9:R.77, 9:H.298 Hydrophobic interactions: 9:V.296, 3:D.85 Salt bridges: 9:R.77

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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