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

The Crystal Structure of Swine Vesicular Disease Virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

6 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 9 PLIP interactions: 9 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: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 SPH.11: 13 residues within 4Å: Chain U: 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 U Hydrophobic interactions: U:T.96, U:L.118, U:Y.145, U:Y.145, U:Y.145, U:V.169, U:V.182 Hydrogen bonds: U:S.192, U:S.192

6 x MYR: MYRISTIC ACID(Non-covalent)

MYR.2: 9 residues within 4Å: Chain D: G.2, I.30, Y.32 Chain H: A.3, T.28, N.29, I.30, Y.32 Ligands: MYR.4 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:I.30, D:Y.32 Hydrogen bonds: H:T.28, D:G.2 MYR.4: 4 residues within 4Å: Chain H: G.2, I.30, Y.32 Ligands: MYR.2 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:Y.32 Hydrogen bonds: H:G.2 MYR.6: 4 residues within 4Å: Chain L: G.2, I.30, Y.32 Ligands: MYR.8 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:Y.32 Hydrogen bonds: L:G.2 MYR.8: 9 residues within 4Å: Chain L: A.3, T.28, N.29, I.30, Y.32 Chain P: G.2, I.30, Y.32 Ligands: MYR.6 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain P Hydrophobic interactions: L:I.30, P:Y.32 Hydrogen bonds: L:T.28, P:G.2 MYR.10: 9 residues within 4Å: Chain T: G.2, I.30, Y.32 Chain X: A.3, T.28, N.29, I.30, Y.32 Ligands: MYR.12 3 PLIP interactions: 2 interactions with chain T, 1 interactions with chain X Hydrophobic interactions: T:Y.32, X:I.30 Hydrogen bonds: T:G.2 MYR.12: 4 residues within 4Å: Chain X: G.2, I.30, Y.32 Ligands: MYR.10 2 PLIP interactions: 2 interactions with chain X Hydrophobic interactions: X:Y.32 Hydrogen bonds: X: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: AEIMQU
Coat protein VP2: BFJNRV
Coat protein VP3: CGKOSW
Coat protein VP4: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

U
A

B
B

F
B

J
B

N
B

R
B

V
B

C
C

G
C

K
C

O
C

S
C

W
C

D
D

H
D

L
D

P
D

T
D

X
D

Coat protein VP1

Coat protein VP2

Coat protein VP3

Coat protein VP4

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