SMTL ID : 4gb3.5 (4 other biounits)

Human coxsackievirus B3 strain RD coat protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

hetero-10-10-10-10-mer

Ligands

10 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 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 PLM.13: 10 residues within 4Å: Chain Y: 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 Y Hydrophobic interactions: Y:I.92, Y:I.92, Y:P.94, Y:L.116, Y:Y.143, Y:Y.143 Hydrogen bonds: Y:N.211 Salt bridges: Y:R.95 PLM.15: 10 residues within 4Å: Chain 2: 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 2 Hydrophobic interactions: 2:I.92, 2:I.92, 2:P.94, 2:L.116, 2:Y.143, 2:Y.143 Hydrogen bonds: 2:N.211 Salt bridges: 2:R.95 PLM.17: 10 residues within 4Å: Chain 6: 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 6 Hydrophobic interactions: 6:I.92, 6:I.92, 6:P.94, 6:L.116, 6:Y.143, 6:Y.143 Hydrogen bonds: 6:N.211 Salt bridges: 6:R.95 PLM.19: 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 7 PLIP interactions: 7 interactions with chain a Hydrophobic interactions: a:I.92, a:I.92, a:L.116, a:Y.143, a:Y.143 Hydrogen bonds: a:N.211 Salt bridges: a:R.95

10 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: 2 interactions with chain D, 1 interactions with chain H, 1 interactions with chain K, 1 interactions with chain G Hydrophobic interactions: D:I.29, H:T.27, K:L.2, G: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: 1 interactions with chain O, 2 interactions with chain H, 1 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: O:L.2, H:I.29, L:T.27, 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: 1 interactions with chain S, 1 interactions with chain O, 2 interactions with chain L, 1 interactions with chain P Hydrophobic interactions: S:L.2, O:L.2, L:I.29, P:T.27 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 S, 2 interactions with chain P, 1 interactions with chain T, 1 interactions with chain C Hydrophobic interactions: S:L.2, P:I.29, T:T.27, C:L.2 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: 2 interactions with chain T, 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: T:I.29, D:T.27, C:L.2, G:L.2 Hydrogen bonds: T:A.2 MYR.12: 11 residues within 4Å: Chain 0: L.2 Chain 1: T.27 Chain 4: L.2 Chain 8: L.2 Chain X: G.1, A.2, I.29 Ligands: MYR.14, MYR.16, MYR.18, MYR.20 5 PLIP interactions: 1 interactions with chain 4, 1 interactions with chain 1, 1 interactions with chain 0, 2 interactions with chain X Hydrophobic interactions: 4:L.2, 1:T.27, 0:L.2, X:I.29 Hydrogen bonds: X:A.2 MYR.14: 11 residues within 4Å: Chain 1: G.1, A.2, I.29 Chain 4: L.2 Chain 5: T.27 Chain 8: L.2 Ligands: MYR.12, MYR.16, MYR.18, MYR.20 Chain c: L.2 5 PLIP interactions: 2 interactions with chain 1, 1 interactions with chain 4, 1 interactions with chain 5, 1 interactions with chain 8 Hydrophobic interactions: 1:I.29, 4:L.2, 5:T.27, 8:L.2 Hydrogen bonds: 1:A.2 MYR.16: 11 residues within 4Å: Chain 5: G.1, A.2, I.29 Chain 8: L.2 Chain 9: T.27 Chain W: L.2 Ligands: MYR.12, MYR.14, MYR.18, MYR.20 Chain c: L.2 5 PLIP interactions: 2 interactions with chain 5, 1 interactions with chain 8, 1 interactions with chain 9, 1 interactions with chain c Hydrophobic interactions: 5:I.29, 8:L.2, 9:T.27, c:L.2 Hydrogen bonds: 5:A.2 MYR.18: 11 residues within 4Å: Chain 0: L.2 Chain 9: G.1, A.2, I.29 Chain W: L.2 Ligands: MYR.12, MYR.14, MYR.16, MYR.20 Chain c: L.2 Chain d: T.27 5 PLIP interactions: 2 interactions with chain 9, 1 interactions with chain d, 1 interactions with chain W, 1 interactions with chain c Hydrophobic interactions: 9:I.29, d:T.27, W:L.2, c:L.2 Hydrogen bonds: 9:A.2 MYR.20: 11 residues within 4Å: Chain 0: L.2 Chain 4: L.2 Chain W: L.2 Chain X: T.27 Ligands: MYR.12, MYR.14, MYR.16, MYR.18 Chain d: G.1, A.2, I.29 5 PLIP interactions: 1 interactions with chain X, 2 interactions with chain d, 1 interactions with chain W, 1 interactions with chain 0 Hydrophobic interactions: X:T.27, d:I.29, W:L.2, 0:L.2 Hydrogen bonds: d: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: AEIMQUY26a
coat protein 2: BFJNRVZ37b
coat protein 3: CGKOSW048c
coat protein 4: DHLPTX159d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

E
1

I
1

M
1

Q
1

U
1

Y
1

2
1

6
1

a
1

B
2

F
2

J
2

N
2

R
2

V
2

Z
2

3
2

7
2

b
2

C
3

G
3

K
3

O
3

S
3

W
3

0
3

4
3

8
3

c
3

D
4

H
4

L
4

P
4

T
4

X
4

1
4

5
4

9
4

d
4

coat protein 1

coat protein 2

coat protein 3

coat protein 4

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