SMTL ID : 5abj.2 (3 other biounits)

Structure of Coxsackievirus A16 in complex with GPP3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-oligomer

Ligands

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: L.89, R.250 Chain Q: R.236 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.236 Chain E: L.89, R.250 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain E: R.236 Chain I: L.89, R.250 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain I: R.236 Chain M: L.89, R.250 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain M: R.236 Chain Q: L.89, R.250 Ligand excluded by PLIP

5 x YM2: 1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE(Non-covalent)

YM2.2: 18 residues within 4Å: Chain A: I.111, D.112, L.113, M.114, F.135, F.137, Y.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.111, A:L.113, A:F.135, A:F.135, A:Y.155, A:Y.155, A:V.179, A:V.192, A:W.203, A:N.228, A:M.230 Hydrogen bonds: A:L.113 YM2.5: 18 residues within 4Å: Chain E: I.111, D.112, L.113, M.114, F.135, F.137, Y.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:I.111, E:L.113, E:F.135, E:F.135, E:Y.155, E:Y.155, E:V.179, E:V.192, E:W.203, E:N.228, E:M.230 Hydrogen bonds: E:L.113 YM2.8: 18 residues within 4Å: Chain I: I.111, D.112, L.113, M.114, F.135, F.137, Y.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:I.111, I:L.113, I:F.135, I:F.135, I:Y.155, I:Y.155, I:V.179, I:V.192, I:W.203, I:N.228, I:M.230 Hydrogen bonds: I:L.113 YM2.11: 18 residues within 4Å: Chain M: I.111, D.112, L.113, M.114, F.135, F.137, Y.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230 12 PLIP interactions: 12 interactions with chain M Hydrophobic interactions: M:I.111, M:L.113, M:F.135, M:F.135, M:Y.155, M:Y.155, M:V.179, M:V.192, M:W.203, M:N.228, M:M.230 Hydrogen bonds: M:L.113 YM2.14: 18 residues within 4Å: Chain Q: I.111, D.112, L.113, M.114, F.135, F.137, Y.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.230 12 PLIP interactions: 12 interactions with chain Q Hydrophobic interactions: Q:I.111, Q:L.113, Q:F.135, Q:F.135, Q:Y.155, Q:Y.155, Q:V.179, Q:V.192, Q:W.203, Q:N.228, Q:M.230 Hydrogen bonds: Q:L.113

5 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain C: P.8 Chain G: E.5 Chain K: G.1 Chain Q: Q.189 Chain S: V.20, S.21 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain Q Hydrogen bonds: K:G.1, Q:Q.189 NA.6: 6 residues within 4Å: Chain A: Q.189 Chain C: V.20, S.21 Chain G: P.8 Chain K: E.5 Chain O: G.1 2 PLIP interactions: 1 interactions with chain O, 1 interactions with chain K Hydrogen bonds: O:G.1, K:E.5 NA.9: 6 residues within 4Å: Chain E: Q.189 Chain G: V.20, S.21 Chain K: P.8 Chain O: E.5 Chain S: G.1 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain S Hydrogen bonds: K:P.8, S:G.1 NA.12: 6 residues within 4Å: Chain C: G.1 Chain I: Q.189 Chain K: V.20, S.21 Chain O: P.8 Chain S: E.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.1, C:G.1 NA.15: 6 residues within 4Å: Chain C: E.5 Chain G: G.1 Chain M: Q.189 Chain O: V.20, S.21 Chain S: P.8 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain O Hydrogen bonds: G:G.1, O:S.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Colibus, L. et al., Structure Elucidation of Coxsackievirus A16 in Complex with Gpp3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses. Plos Pathog. (2015)

Release Date

2015-09-09

Peptides

VP1: AEIMQ
VP2: BFJNR
VP3: CGKOS
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

VP1

VP2

VP3

VP4

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