SMTL ID : 4gb3.3 (4 other biounits)

Human coxsackievirus B3 strain RD coat protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

6 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 10 residues within 4Å: Chain A: I.92, P.94, R.95, L.116, Y.143, P.165, M.178, L.210, N.211, M.213 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.92, A:I.92, A:P.94, A:L.116, A:Y.143, A:Y.143 Hydrogen bonds: A:N.211 Salt bridges: A:R.95 PLM.3: 10 residues within 4Å: Chain E: I.92, P.94, R.95, L.116, Y.143, P.165, M.178, L.210, N.211, M.213 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.92, E:I.92, E:P.94, E:L.116, E:Y.143, E:Y.143 Hydrogen bonds: E:N.211 Salt bridges: E:R.95 PLM.5: 10 residues within 4Å: Chain I: I.92, P.94, R.95, L.116, Y.143, P.165, M.178, L.210, N.211, M.213 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:I.92, I:I.92, I:P.94, I:L.116, I:Y.143, I:Y.143 Hydrogen bonds: I:N.211 Salt bridges: I:R.95 PLM.7: 10 residues within 4Å: Chain M: I.92, P.94, R.95, L.116, Y.143, P.165, M.178, L.210, N.211, M.213 7 PLIP interactions: 7 interactions with chain M Hydrophobic interactions: M:I.92, M:I.92, M:L.116, M:Y.143, M:Y.143 Hydrogen bonds: M:N.211 Salt bridges: M:R.95 PLM.9: 10 residues within 4Å: Chain Q: I.92, P.94, R.95, L.116, Y.143, P.165, M.178, L.210, N.211, M.213 8 PLIP interactions: 8 interactions with chain Q Hydrophobic interactions: Q:I.92, Q:I.92, Q:P.94, Q:L.116, Q:Y.143, Q:Y.143 Hydrogen bonds: Q:N.211 Salt bridges: Q:R.95 PLM.11: 10 residues within 4Å: Chain U: I.92, P.94, R.95, L.116, Y.143, P.165, M.178, L.210, N.211, M.213 8 PLIP interactions: 8 interactions with chain U Hydrophobic interactions: U:I.92, U:I.92, U:P.94, U:L.116, U:Y.143, U:Y.143 Hydrogen bonds: U:N.211 Salt bridges: U:R.95

6 x MYR: MYRISTIC ACID(Covalent)

MYR.2: 6 residues within 4Å: Chain D: G.1, A.2, I.29 Chain G: L.2 Chain H: T.27 Ligands: MYR.4 4 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G, 2 interactions with chain D Hydrophobic interactions: H:T.27, G:L.2, D:I.29 Hydrogen bonds: D:A.2 MYR.4: 4 residues within 4Å: Chain H: G.1, A.2, I.29 Ligands: MYR.2 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:I.29 Hydrogen bonds: H:A.2 MYR.6: 4 residues within 4Å: Chain L: G.1, A.2, I.29 Ligands: MYR.8 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:I.29 Hydrogen bonds: L:A.2 MYR.8: 6 residues within 4Å: Chain K: L.2 Chain L: T.27 Chain P: G.1, A.2, I.29 Ligands: MYR.6 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K, 2 interactions with chain P Hydrophobic interactions: L:T.27, K:L.2, P:I.29 Hydrogen bonds: P:A.2 MYR.10: 6 residues within 4Å: Chain T: G.1, A.2, I.29 Chain W: L.2 Chain X: T.27 Ligands: MYR.12 4 PLIP interactions: 2 interactions with chain T, 1 interactions with chain X, 1 interactions with chain W Hydrophobic interactions: T:I.29, X:T.27, W:L.2 Hydrogen bonds: T:A.2 MYR.12: 4 residues within 4Å: Chain X: G.1, A.2, I.29 Ligands: MYR.10 2 PLIP interactions: 2 interactions with chain X Hydrophobic interactions: X:I.29 Hydrogen bonds: X:A.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoder, J.D. et al., The Crystal Structure of a Coxsackievirus B3-RD Variant and a Refined 9-Angstrom Cryo-Electron Microscopy Reconstruction of the Virus Complexed with Decay-Accelerating Factor (DAF) Provide a New Footprint of DAF on the Virus Surface. J.Virol. (2012)

Release Date

2012-09-26

Peptides

coat protein 1: AEIMQU
coat protein 2: BFJNRV
coat protein 3: CGKOSW
coat protein 4: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

E
1

I
1

M
1

Q
1

U
1

B
2

F
2

J
2

N
2

R
2

V
2

C
3

G
3

K
3

O
3

S
3

W
3

D
4

H
4

L
4

P
4

T
4

X
4

coat protein 1

coat protein 2

coat protein 3

coat protein 4

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