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

Coxsackievirus B3 in complex with capsid binder compound 17

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-6-mer

Ligands

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

FHK.1: 8 residues within 4Å: Chain A: C.61, F.64, E.66, R.222 Chain C: Q.233, Q.234, N.235, F.236 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.236, A:F.64 Hydrogen bonds: C:Q.233 pi-Stacking: C:F.236, A:F.64 Salt bridges: A:R.222 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 I: C.61, F.64, E.66, R.222 Chain K: Q.233, Q.234, N.235, F.236 Chain M: D.143, S.144, Y.145, W.147, Q.148, R.207 9 PLIP interactions: 3 interactions with chain I, 3 interactions with chain K, 3 interactions with chain M Hydrophobic interactions: I:F.64, K:F.236, M:Q.148 Salt bridges: I:R.222, M:R.207 pi-Stacking: I:F.64, K:F.236 Hydrogen bonds: K:Q.233, M:Q.148 FHK.7: 8 residues within 4Å: Chain M: C.61, F.64, E.66, R.222 Chain O: Q.233, Q.234, N.235, F.236 6 PLIP interactions: 3 interactions with chain O, 3 interactions with chain M Hydrophobic interactions: O:F.236, M:F.64 Hydrogen bonds: O:Q.233 pi-Stacking: O:F.236, M:F.64 Salt bridges: M:R.222 FHK.9: 8 residues within 4Å: Chain Q: C.61, F.64, E.66, R.222 Chain S: Q.233, Q.234, N.235, F.236 6 PLIP interactions: 3 interactions with chain S, 3 interactions with chain Q Hydrophobic interactions: S:F.236, Q:F.64 Hydrogen bonds: S:Q.233 pi-Stacking: S:F.236, Q:F.64 Salt bridges: Q:R.222 FHK.11: 14 residues within 4Å: Chain Q: D.143, S.144, Y.145, W.147, Q.148, R.207 Chain U: C.61, F.64, E.66, R.222 Chain W: Q.233, Q.234, N.235, F.236 9 PLIP interactions: 3 interactions with chain Q, 3 interactions with chain W, 3 interactions with chain U Hydrophobic interactions: Q:Q.148, W:F.236, U:F.64 Hydrogen bonds: Q:Q.148, W:Q.233 Salt bridges: Q:R.207, U:R.222 pi-Stacking: W:F.236, U:F.64

6 x MYR: MYRISTIC ACID(Covalent)

MYR.2: 5 residues within 4Å: Chain D: G.1, A.2, Y.31 Chain H: T.27, I.29 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:I.29, D:Y.31, D:Y.31 MYR.4: 3 residues within 4Å: Chain H: G.1, A.2, Y.31 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:Y.31, H:Y.31 MYR.6: 3 residues within 4Å: Chain L: G.1, A.2, Y.31 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:Y.31, L:Y.31 MYR.8: 5 residues within 4Å: Chain L: T.27, I.29 Chain P: G.1, A.2, Y.31 3 PLIP interactions: 2 interactions with chain P, 1 interactions with chain L Hydrophobic interactions: P:Y.31, P:Y.31, L:I.29 MYR.10: 5 residues within 4Å: Chain T: G.1, A.2, Y.31 Chain X: T.27, I.29 3 PLIP interactions: 1 interactions with chain X, 2 interactions with chain T Hydrophobic interactions: X:I.29, T:Y.31, T:Y.31 MYR.12: 3 residues within 4Å: Chain X: G.1, A.2, Y.31 2 PLIP interactions: 2 interactions with chain X Hydrophobic interactions: X:Y.31, X:Y.31

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: AEIMQU
capsid protein VP2: BFJNRV
capsid protein VP3: CGKOSW
capsid 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

capsid protein VP1

capsid protein VP2

capsid protein VP3

capsid protein VP4

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