SMTL ID : 1oop.2 (3 other biounits)

The Crystal Structure of Swine Vesicular Disease Virus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-5-5-5-5-mer

Ligands

5 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 13 residues within 4Å: Chain A: I.94, T.96, L.116, L.118, Y.145, P.167, V.169, M.180, V.182, Y.191, S.192, I.209, M.215 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.96, A:L.118, A:Y.145, A:Y.145, A:Y.145, A:V.169, A:V.182 Hydrogen bonds: A:S.192, A:S.192 SPH.3: 13 residues within 4Å: Chain E: I.94, T.96, L.116, L.118, Y.145, P.167, V.169, M.180, V.182, Y.191, S.192, I.209, M.215 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:T.96, E:L.118, E:Y.145, E:Y.145, E:Y.145, E:V.169, E:V.182 Hydrogen bonds: E:T.96, E:S.192, E:S.192 SPH.5: 13 residues within 4Å: Chain I: I.94, T.96, L.116, L.118, Y.145, P.167, V.169, M.180, V.182, Y.191, S.192, I.209, M.215 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:T.96, I:L.118, I:Y.145, I:Y.145, I:Y.145, I:V.169, I:V.182 Hydrogen bonds: I:T.96, I:S.192, I:S.192 SPH.7: 13 residues within 4Å: Chain M: I.94, T.96, L.116, L.118, Y.145, P.167, V.169, M.180, V.182, Y.191, S.192, I.209, M.215 9 PLIP interactions: 9 interactions with chain M Hydrophobic interactions: M:T.96, M:L.118, M:Y.145, M:Y.145, M:Y.145, M:V.169, M:V.182 Hydrogen bonds: M:S.192, M:S.192 SPH.9: 13 residues within 4Å: Chain Q: I.94, T.96, L.116, L.118, Y.145, P.167, V.169, M.180, V.182, Y.191, S.192, I.209, M.215 9 PLIP interactions: 9 interactions with chain Q Hydrophobic interactions: Q:T.96, Q:L.118, Q:Y.145, Q:Y.145, Q:Y.145, Q:V.169, Q:V.182 Hydrogen bonds: Q:S.192, Q:S.192

5 x MYR: MYRISTIC ACID(Non-covalent)

MYR.2: 11 residues within 4Å: Chain D: G.2, I.30, Y.32 Chain H: A.3, T.28, N.29, I.30, Y.32 Chain O: L.2 Ligands: MYR.4, MYR.10 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain O, 2 interactions with chain D Hydrophobic interactions: H:I.30, O:L.2, D:Y.32 Hydrogen bonds: H:T.28, D:G.2 MYR.4: 11 residues within 4Å: Chain H: G.2, I.30, Y.32 Chain L: A.3, T.28, N.29, I.30, Y.32 Chain S: L.2 Ligands: MYR.2, MYR.6 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain S, 2 interactions with chain L Hydrophobic interactions: H:Y.32, S:L.2, L:I.30 Hydrogen bonds: H:G.2, L:T.28 MYR.6: 11 residues within 4Å: Chain C: L.2 Chain L: G.2, I.30, Y.32 Chain P: A.3, T.28, N.29, I.30, Y.32 Ligands: MYR.4, MYR.8 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain C, 2 interactions with chain P Hydrophobic interactions: L:Y.32, C:L.2, P:I.30 Hydrogen bonds: L:G.2, P:T.28 MYR.8: 11 residues within 4Å: Chain G: L.2 Chain P: G.2, I.30, Y.32 Chain T: A.3, T.28, N.29, I.30, Y.32 Ligands: MYR.6, MYR.10 4 PLIP interactions: 1 interactions with chain T, 2 interactions with chain P, 1 interactions with chain G Hydrophobic interactions: T:I.30, P:Y.32, G:L.2 Hydrogen bonds: P:G.2 MYR.10: 11 residues within 4Å: Chain D: A.3, T.28, N.29, I.30, Y.32 Chain K: L.2 Chain T: G.2, I.30, Y.32 Ligands: MYR.2, MYR.8 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain D, 2 interactions with chain T Hydrophobic interactions: K:L.2, D:I.30, T:Y.32 Hydrogen bonds: T:G.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fry, E.E. et al., Crystal Structure of Swine Vesicular Disease Virus and Implications for Host Adaptation. J.Virol. (2003)

Release Date

2003-04-22

Peptides

Coat protein VP1: AEIMQ
Coat protein VP2: BFJNR
Coat protein VP3: CGKOS
Coat protein VP4: DHLPT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

B
B

F
B

J
B

N
B

R
B

C
C

G
C

K
C

O
C

S
C

D
D

H
D

L
D

P
D

T
D

Coat protein VP1

Coat protein VP2

Coat protein VP3

Coat protein VP4

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