SMTL ID : 3vbh.5 (4 other biounits)

Crystal structure of formaldehyde treated human enterovirus 71 (space group R32)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-10-10-10-10-mer

Ligands

10 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 14 residues within 4Å: Chain A: I.111, D.112, I.113, F.135, F.137, F.155, V.179, V.192, M.195, W.203, N.228, M.230, F.233, A.275 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.111, A:F.135, A:F.137, A:F.155, A:F.155, A:V.179, A:V.192, A:W.203, A:N.228, A:F.233, A:F.233 Hydrogen bonds: A:D.112, A:I.113 Water bridges: A:N.228 SPH.6: 14 residues within 4Å: Chain E: I.111, D.112, I.113, F.135, F.137, F.155, V.179, V.192, M.195, W.203, N.228, M.230, F.233, A.275 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:I.111, E:F.135, E:F.137, E:F.155, E:F.155, E:V.179, E:V.192, E:W.203, E:N.228, E:F.233, E:F.233 Hydrogen bonds: E:D.112, E:I.113 Water bridges: E:N.228 SPH.11: 14 residues within 4Å: Chain I: I.111, D.112, I.113, F.135, F.137, F.155, V.179, V.192, M.195, W.203, N.228, M.230, F.233, A.275 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:I.111, I:F.135, I:F.137, I:F.155, I:F.155, I:V.179, I:V.192, I:W.203, I:N.228, I:F.233, I:F.233 Hydrogen bonds: I:D.112, I:I.113 Water bridges: I:N.228 SPH.16: 14 residues within 4Å: Chain M: I.111, D.112, I.113, F.135, F.137, F.155, V.179, V.192, M.195, W.203, N.228, M.230, F.233, A.275 14 PLIP interactions: 14 interactions with chain M Hydrophobic interactions: M:I.111, M:F.135, M:F.137, M:F.155, M:F.155, M:V.179, M:V.192, M:W.203, M:N.228, M:F.233, M:F.233 Hydrogen bonds: M:D.112, M:I.113 Water bridges: M:N.228 SPH.21: 14 residues within 4Å: Chain Q: I.111, D.112, I.113, F.135, F.137, F.155, V.179, V.192, M.195, W.203, N.228, M.230, F.233, A.275 14 PLIP interactions: 14 interactions with chain Q Hydrophobic interactions: Q:I.111, Q:F.135, Q:F.137, Q:F.155, Q:F.155, Q:V.179, Q:V.192, Q:W.203, Q:N.228, Q:F.233, Q:F.233 Hydrogen bonds: Q:D.112, Q:I.113 Water bridges: Q:N.228 SPH.26: 14 residues within 4Å: Chain U: I.111, D.112, I.113, F.135, F.137, F.155, V.179, V.192, M.195, W.203, N.228, M.230, F.233, A.275 14 PLIP interactions: 14 interactions with chain U Hydrophobic interactions: U:I.111, U:F.135, U:F.137, U:F.155, U:F.155, U:V.179, U:V.192, U:W.203, U:N.228, U:F.233, U:F.233 Hydrogen bonds: U:D.112, U:I.113 Water bridges: U:N.228 SPH.31: 14 residues within 4Å: Chain Y: I.111, D.112, I.113, F.135, F.137, F.155, V.179, V.192, M.195, W.203, N.228, M.230, F.233, A.275 14 PLIP interactions: 14 interactions with chain Y Hydrophobic interactions: Y:I.111, Y:F.135, Y:F.137, Y:F.155, Y:F.155, Y:V.179, Y:V.192, Y:W.203, Y:N.228, Y:F.233, Y:F.233 Hydrogen bonds: Y:D.112, Y:I.113 Water bridges: Y:N.228 SPH.36: 14 residues within 4Å: Chain 2: I.111, D.112, I.113, F.135, F.137, F.155, V.179, V.192, M.195, W.203, N.228, M.230, F.233, A.275 14 PLIP interactions: 14 interactions with chain 2 Hydrophobic interactions: 2:I.111, 2:F.135, 2:F.137, 2:F.155, 2:F.155, 2:V.179, 2:V.192, 2:W.203, 2:N.228, 2:F.233, 2:F.233 Hydrogen bonds: 2:D.112, 2:I.113 Water bridges: 2:N.228 SPH.41: 14 residues within 4Å: Chain 6: I.111, D.112, I.113, F.135, F.137, F.155, V.179, V.192, M.195, W.203, N.228, M.230, F.233, A.275 14 PLIP interactions: 14 interactions with chain 6 Hydrophobic interactions: 6:I.111, 6:F.135, 6:F.137, 6:F.155, 6:F.155, 6:V.179, 6:V.192, 6:W.203, 6:N.228, 6:F.233, 6:F.233 Hydrogen bonds: 6:D.112, 6:I.113 Water bridges: 6:N.228 SPH.46: 14 residues within 4Å: Chain a: I.111, D.112, I.113, F.135, F.137, F.155, V.179, V.192, M.195, W.203, N.228, M.230, F.233, A.275 14 PLIP interactions: 14 interactions with chain a Hydrophobic interactions: a:I.111, a:F.135, a:F.137, a:F.155, a:F.155, a:V.179, a:V.192, a:W.203, a:N.228, a:F.233, a:F.233 Hydrogen bonds: a:D.112, a:I.113 Water bridges: a:N.228

20 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: T.28, G.29, N.31, N.71 Ligand excluded by PLIP K.4: 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 Ligand excluded by PLIP K.7: 4 residues within 4Å: Chain E: T.28, G.29, N.31, N.71 Ligand excluded by PLIP K.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 Ligand excluded by PLIP K.12: 4 residues within 4Å: Chain I: T.28, G.29, N.31, N.71 Ligand excluded by PLIP K.14: 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 Ligand excluded by PLIP K.17: 4 residues within 4Å: Chain M: T.28, G.29, N.31, N.71 Ligand excluded by PLIP K.19: 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 Ligand excluded by PLIP K.22: 4 residues within 4Å: Chain Q: T.28, G.29, N.31, N.71 Ligand excluded by PLIP K.24: 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 Ligand excluded by PLIP K.27: 4 residues within 4Å: Chain U: T.28, G.29, N.31, N.71 Ligand excluded by PLIP K.29: 6 residues within 4Å: Chain 0: P.8 Chain 4: E.5 Chain 8: G.1 Chain U: Q.189 Chain W: V.20, S.21 Ligand excluded by PLIP K.32: 4 residues within 4Å: Chain Y: T.28, G.29, N.31, N.71 Ligand excluded by PLIP K.34: 6 residues within 4Å: Chain 0: V.20, S.21 Chain 4: P.8 Chain 8: E.5 Chain Y: Q.189 Chain c: G.1 Ligand excluded by PLIP K.37: 4 residues within 4Å: Chain 2: T.28, G.29, N.31, N.71 Ligand excluded by PLIP K.39: 6 residues within 4Å: Chain 2: Q.189 Chain 4: V.20, S.21 Chain 8: P.8 Chain W: G.1 Chain c: E.5 Ligand excluded by PLIP K.42: 4 residues within 4Å: Chain 6: T.28, G.29, N.31, N.71 Ligand excluded by PLIP K.44: 6 residues within 4Å: Chain 0: G.1 Chain 6: Q.189 Chain 8: V.20, S.21 Chain W: E.5 Chain c: P.8 Ligand excluded by PLIP K.47: 4 residues within 4Å: Chain a: T.28, G.29, N.31, N.71 Ligand excluded by PLIP K.49: 6 residues within 4Å: Chain 0: E.5 Chain 4: G.1 Chain W: P.8 Chain a: Q.189 Chain c: V.20, S.21 Ligand excluded by PLIP

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

NA.3: 7 residues within 4Å: Chain A: V.44, P.45, L.47, Q.48 Chain D: E.52, A.54, P.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.45, A:Q.48 NA.8: 7 residues within 4Å: Chain E: V.44, P.45, L.47, Q.48 Chain H: E.52, A.54, P.56 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.47, E:Q.48 NA.13: 7 residues within 4Å: Chain I: V.44, P.45, L.47, Q.48 Chain L: E.52, A.54, P.56 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:L.47, I:Q.48 NA.18: 7 residues within 4Å: Chain M: V.44, P.45, L.47, Q.48 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.23: 7 residues within 4Å: Chain Q: V.44, P.45, L.47, Q.48 Chain T: E.52, A.54, P.56 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:V.44, Q:Q.48 NA.28: 7 residues within 4Å: Chain U: V.44, P.45, L.47, Q.48 Chain X: E.52, A.54, P.56 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:V.44, U:Q.48 NA.33: 7 residues within 4Å: Chain 1: E.52, A.54, P.56 Chain Y: V.44, P.45, L.47, Q.48 2 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain 1 Hydrogen bonds: Y:Q.48, 1:E.52 NA.38: 7 residues within 4Å: Chain 2: V.44, P.45, L.47, Q.48 Chain 5: E.52, A.54, P.56 2 PLIP interactions: 1 interactions with chain 2, 1 interactions with chain 5 Hydrogen bonds: 2:Q.48, 5:A.54 NA.43: 7 residues within 4Å: Chain 6: V.44, P.45, L.47, Q.48 Chain 9: E.52, A.54, P.56 2 PLIP interactions: 2 interactions with chain 6 Hydrogen bonds: 6:L.47, 6:Q.48 NA.48: 7 residues within 4Å: Chain a: V.44, P.45, L.47, Q.48 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

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

CL.5: 6 residues within 4Å: Chain C: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain G: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain K: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain O: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain S: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.30: 6 residues within 4Å: Chain W: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.35: 6 residues within 4Å: Chain 0: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.40: 6 residues within 4Å: Chain 4: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.45: 6 residues within 4Å: Chain 8: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.50: 6 residues within 4Å: Chain c: 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: AEIMQUY26a
Genome polyprotein, capsid protein VP2: BFJNRVZ37b
Genome Polyprotein, vapsid protein VP3: CGKOSW048c
Genome Polyprotein, capsid protein VP4: DHLPTX159d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

U
A

Y
A

2
A

6
A

a
A

B
B

F
B

J
B

N
B

R
B

V
B

Z
B

3
B

7
B

b
B

C
C

G
C

K
C

O
C

S
C

W
C

0
C

4
C

8
C

c
C

D
D

H
D

L
D

P
D

T
D

X
D

1
D

5
D

9
D

d
D

Genome Polyprotein, capsid protein VP1

Genome polyprotein, capsid protein VP2

Genome Polyprotein, vapsid protein VP3

Genome Polyprotein, capsid protein VP4

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