SMTL ID : 3vbf.2 (3 other biounits)

Crystal structure of formaldehyde treated human Enterovirus 71 (space group I23)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-5-5-5-5-mer

Ligands

5 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 11 residues within 4Å: Chain A: I.111, D.112, I.113, F.135, F.155, M.195, W.203, N.228, M.230, F.233, A.275 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.111, A:I.111, A:F.135, A:F.155, A:W.203, A:N.228, A:F.233, A:F.233 Hydrogen bonds: A:D.112, A:D.112, A:I.113 SPH.7: 11 residues within 4Å: Chain E: I.111, D.112, I.113, F.135, F.155, M.195, W.203, N.228, M.230, F.233, A.275 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:I.111, E:I.111, E:F.135, E:F.155, E:W.203, E:N.228, E:F.233, E:F.233 Hydrogen bonds: E:D.112, E:D.112, E:I.113 SPH.13: 11 residues within 4Å: Chain I: I.111, D.112, I.113, F.135, F.155, M.195, W.203, N.228, M.230, F.233, A.275 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:I.111, I:I.111, I:F.135, I:F.155, I:W.203, I:N.228, I:F.233, I:F.233 Hydrogen bonds: I:D.112, I:I.113 SPH.19: 11 residues within 4Å: Chain M: I.111, D.112, I.113, F.135, F.155, M.195, W.203, N.228, M.230, F.233, A.275 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:I.111, M:I.111, M:F.135, M:F.155, M:W.203, M:N.228, M:F.233, M:F.233 Hydrogen bonds: M:D.112, M:I.113 SPH.25: 11 residues within 4Å: Chain Q: I.111, D.112, I.113, F.135, F.155, M.195, W.203, N.228, M.230, F.233, A.275 11 PLIP interactions: 11 interactions with chain Q Hydrophobic interactions: Q:I.111, Q:I.111, Q:F.135, Q:F.155, Q:W.203, Q:N.228, Q:F.233, Q:F.233 Hydrogen bonds: Q:D.112, Q:D.112, Q:I.113

5 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 7 residues within 4Å: Chain A: P.25, A.26, T.28, Q.30 Chain C: Q.48, K.222 Chain D: P.39 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:P.25, A:Q.30, C:Q.48 AMP.8: 7 residues within 4Å: Chain E: P.25, A.26, T.28, Q.30 Chain G: Q.48, K.222 Chain H: P.39 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G Hydrogen bonds: E:P.25, E:Q.30, G:Q.48 AMP.14: 7 residues within 4Å: Chain I: P.25, A.26, T.28, Q.30 Chain K: Q.48, K.222 Chain L: P.39 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain K Hydrogen bonds: I:P.25, I:Q.30, K:K.222 AMP.20: 7 residues within 4Å: Chain M: P.25, A.26, T.28, Q.30 Chain O: Q.48, K.222 Chain P: P.39 3 PLIP interactions: 1 interactions with chain O, 2 interactions with chain M Hydrogen bonds: O:Q.48, M:P.25, M:Q.30 AMP.26: 7 residues within 4Å: Chain Q: P.25, A.26, T.28, Q.30 Chain S: Q.48, K.222 Chain T: P.39 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain S Hydrogen bonds: Q:P.25, Q:Q.30, S:K.222

10 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: T.28, G.29, N.31, N.71 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.28, A:G.29, A:N.71 K.5: 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 K, 1 interactions with chain G Metal complexes: K:E.5, G:P.8 K.9: 4 residues within 4Å: Chain E: T.28, G.29, N.31, N.71 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.28, E:G.29, E:N.71 K.11: 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 O Metal complexes: K:P.8, O:E.5 K.15: 4 residues within 4Å: Chain I: T.28, G.29, N.31, N.71 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:T.28, I:G.29, I:N.71 K.17: 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: 1 interactions with chain S, 1 interactions with chain O Metal complexes: S:E.5, O:P.8 K.21: 4 residues within 4Å: Chain M: T.28, G.29, N.31, N.71 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:T.28, M:G.29, M:N.71 K.23: 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 C, 1 interactions with chain S Metal complexes: C:E.5, S:P.8 K.27: 4 residues within 4Å: Chain Q: T.28, G.29, N.31, N.71 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:T.28, Q:G.29, Q:N.71 K.29: 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 G, 1 interactions with chain C Metal complexes: G:E.5, C:P.8

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

NA.4: 8 residues within 4Å: Chain A: V.44, P.45, L.47, Q.48, N.57 Chain D: E.52, A.54, P.56 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.52, A:Q.48 NA.10: 8 residues within 4Å: Chain E: V.44, P.45, L.47, Q.48, N.57 Chain H: E.52, A.54, P.56 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.48, E:N.57 NA.16: 8 residues within 4Å: Chain I: V.44, P.45, L.47, Q.48, N.57 Chain L: E.52, A.54, P.56 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I Hydrogen bonds: L:A.54, I:Q.48 NA.22: 8 residues within 4Å: Chain M: V.44, P.45, L.47, Q.48, N.57 Chain P: E.52, A.54, P.56 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:L.47, M:Q.48 NA.28: 8 residues within 4Å: Chain Q: V.44, P.45, L.47, Q.48, N.57 Chain T: E.52, A.54, P.56 2 PLIP interactions: 1 interactions with chain T, 1 interactions with chain Q Hydrogen bonds: T:E.52, Q:Q.48

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

CL.6: 6 residues within 4Å: Chain C: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain G: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain K: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.24: 6 residues within 4Å: Chain O: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.30: 6 residues within 4Å: Chain S: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-02-29

Peptides

Genome Polyprotein, capsid protein VP1: AEIMQ
Genome Polyprotein, capsid protein VP2: BFJNR
Genome Polyprotein, capsid protein VP3: CGKOS
Genome Polyprotein, 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

Genome Polyprotein, capsid protein VP1

Genome Polyprotein, capsid protein VP2

Genome Polyprotein, capsid protein VP3

Genome Polyprotein, capsid protein VP4

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