SMTL ID : 4gb3.2 (4 other biounits)

Human coxsackievirus B3 strain RD coat protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

hetero-5-5-5-5-mer

Ligands

5 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 8 PLIP interactions: 8 interactions with chain M Hydrophobic interactions: M:I.92, M:I.92, M:P.94, 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

5 x MYR: MYRISTIC ACID(Covalent)

MYR.2: 11 residues within 4Å: Chain D: G.1, A.2, I.29 Chain G: L.2 Chain H: T.27 Chain K: L.2 Chain O: L.2 Ligands: MYR.4, MYR.6, MYR.8, MYR.10 5 PLIP interactions: 1 interactions with chain H, 2 interactions with chain D, 1 interactions with chain G, 1 interactions with chain K Hydrophobic interactions: H:T.27, D:I.29, G:L.2, K:L.2 Hydrogen bonds: D:A.2 MYR.4: 11 residues within 4Å: Chain H: G.1, A.2, I.29 Chain K: L.2 Chain L: T.27 Chain O: L.2 Chain S: L.2 Ligands: MYR.2, MYR.6, MYR.8, MYR.10 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain L, 1 interactions with chain O, 1 interactions with chain K Hydrophobic interactions: H:I.29, L:T.27, O:L.2, K:L.2 Hydrogen bonds: H:A.2 MYR.6: 11 residues within 4Å: Chain C: L.2 Chain L: G.1, A.2, I.29 Chain O: L.2 Chain P: T.27 Chain S: L.2 Ligands: MYR.2, MYR.4, MYR.8, MYR.10 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain P, 1 interactions with chain O, 1 interactions with chain S Hydrophobic interactions: L:I.29, P:T.27, O:L.2, S:L.2 Hydrogen bonds: L:A.2 MYR.8: 11 residues within 4Å: Chain C: L.2 Chain G: L.2 Chain P: G.1, A.2, I.29 Chain S: L.2 Chain T: T.27 Ligands: MYR.2, MYR.4, MYR.6, MYR.10 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain P, 1 interactions with chain S, 1 interactions with chain T Hydrophobic interactions: C:L.2, P:I.29, S:L.2, T:T.27 Hydrogen bonds: P:A.2 MYR.10: 11 residues within 4Å: Chain C: L.2 Chain D: T.27 Chain G: L.2 Chain K: L.2 Chain T: G.1, A.2, I.29 Ligands: MYR.2, MYR.4, MYR.6, MYR.8 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 interactions with chain T, 1 interactions with chain G Hydrophobic interactions: C:L.2, D:T.27, T:I.29, G:L.2 Hydrogen bonds: T: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: AEIMQ
coat protein 2: BFJNR
coat protein 3: CGKOS
coat protein 4: DHLPT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

E
1

I
1

M
1

Q
1

B
2

F
2

J
2

N
2

R
2

C
3

G
3

K
3

O
3

S
3

D
4

H
4

L
4

P
4

T
4

coat protein 1

coat protein 2

coat protein 3

coat protein 4

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