SMTL ID : 6zcl.2 (3 other biounits)

Coxsackievirus B3 in complex with capsid binder compound 17

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-5-5-mer

Ligands

5 x FHK: 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid(Non-covalent)

FHK.1: 14 residues within 4Å: Chain A: C.61, F.64, E.66, R.222 Chain C: Q.233, Q.234, N.235, F.236 Chain Q: D.143, S.144, Y.145, W.147, Q.148, R.207 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C, 3 interactions with chain Q Hydrophobic interactions: A:F.64, C:F.236, Q:Q.148 Salt bridges: A:R.222, Q:R.207 pi-Stacking: A:F.64, C:F.236 Hydrogen bonds: C:Q.233, Q:Q.148 FHK.3: 14 residues within 4Å: Chain A: D.143, S.144, Y.145, W.147, Q.148, R.207 Chain E: C.61, F.64, E.66, R.222 Chain G: Q.233, Q.234, N.235, F.236 9 PLIP interactions: 3 interactions with chain G, 3 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: G:F.236, E:F.64, A:Q.148 Hydrogen bonds: G:Q.233, A:Q.148 pi-Stacking: G:F.236, E:F.64 Salt bridges: E:R.222, A:R.207 FHK.5: 14 residues within 4Å: Chain E: D.143, S.144, Y.145, W.147, Q.148, R.207 Chain I: C.61, F.64, E.66, R.222 Chain K: Q.233, Q.234, N.235, F.236 9 PLIP interactions: 3 interactions with chain K, 3 interactions with chain E, 3 interactions with chain I Hydrophobic interactions: K:F.236, E:Q.148, I:F.64 Hydrogen bonds: K:Q.233, E:Q.148 pi-Stacking: K:F.236, I:F.64 Salt bridges: E:R.207, I:R.222 FHK.7: 14 residues within 4Å: Chain I: D.143, S.144, Y.145, W.147, Q.148, R.207 Chain M: C.61, F.64, E.66, R.222 Chain O: Q.233, Q.234, N.235, F.236 9 PLIP interactions: 3 interactions with chain I, 3 interactions with chain O, 3 interactions with chain M Hydrophobic interactions: I:Q.148, O:F.236, M:F.64 Hydrogen bonds: I:Q.148, O:Q.233 Salt bridges: I:R.207, M:R.222 pi-Stacking: O:F.236, M:F.64 FHK.9: 14 residues within 4Å: Chain M: D.143, S.144, Y.145, W.147, Q.148, R.207 Chain Q: C.61, F.64, E.66, R.222 Chain S: Q.233, Q.234, N.235, F.236 9 PLIP interactions: 3 interactions with chain Q, 3 interactions with chain M, 3 interactions with chain S Hydrophobic interactions: Q:F.64, M:Q.148, S:F.236 Salt bridges: Q:R.222, M:R.207 pi-Stacking: Q:F.64, S:F.236 Hydrogen bonds: M:Q.148, S:Q.233

5 x MYR: MYRISTIC ACID(Covalent)

MYR.2: 6 residues within 4Å: Chain D: G.1, A.2, Y.31 Chain H: T.27, I.29 Chain O: L.2 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain O, 1 interactions with chain H Hydrophobic interactions: D:Y.31, D:Y.31, O:L.2, H:I.29 MYR.4: 6 residues within 4Å: Chain H: G.1, A.2, Y.31 Chain L: T.27, I.29 Chain S: L.2 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain S, 2 interactions with chain H Hydrophobic interactions: L:I.29, S:L.2, H:Y.31, H:Y.31 Hydrogen bonds: L:T.27 MYR.6: 6 residues within 4Å: Chain C: L.2 Chain L: G.1, A.2, Y.31 Chain P: T.27, I.29 5 PLIP interactions: 2 interactions with chain P, 2 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: P:I.29, L:Y.31, L:Y.31, C:L.2 Hydrogen bonds: P:T.27 MYR.8: 6 residues within 4Å: Chain G: L.2 Chain P: G.1, A.2, Y.31 Chain T: T.27, I.29 4 PLIP interactions: 2 interactions with chain P, 1 interactions with chain G, 1 interactions with chain T Hydrophobic interactions: P:Y.31, P:Y.31, G:L.2, T:I.29 MYR.10: 6 residues within 4Å: Chain D: T.27, I.29 Chain K: L.2 Chain T: G.1, A.2, Y.31 4 PLIP interactions: 1 interactions with chain K, 2 interactions with chain T, 1 interactions with chain D Hydrophobic interactions: K:L.2, T:Y.31, T:Y.31, D:I.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flatt, J.W. et al., Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses. Commun Biol (2021)

Release Date

2021-03-17

Peptides

capsid protein VP1: AEIMQ
capsid protein VP2: BFJNR
capsid protein VP3: CGKOS
capsid 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

capsid protein VP1

capsid protein VP2

capsid protein VP3

capsid protein VP4

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