SMTL ID : 3vbh.3 (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-6-6-6-6-mer

Ligands

6 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

12 x K: POTASSIUM ION(Non-covalent)

K.2: 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.4: 4 residues within 4Å: Chain A: Q.189 Chain C: V.20, S.21 Chain G: P.8 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:P.8 K.7: 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.9: 3 residues within 4Å: Chain E: Q.189 Chain G: V.20, S.21 No protein-ligand interaction detected (PLIP) K.12: 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.14: 3 residues within 4Å: Chain I: Q.189 Chain K: V.20, S.21 No protein-ligand interaction detected (PLIP) K.17: 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.19: 4 residues within 4Å: Chain K: P.8 Chain M: Q.189 Chain O: V.20, S.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:P.8 K.22: 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.24: 4 residues within 4Å: Chain Q: Q.189 Chain S: V.20, S.21 Chain W: P.8 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:P.8 K.27: 4 residues within 4Å: Chain U: T.28, G.29, N.31, N.71 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:T.28, U:G.29, U:N.71 K.29: 3 residues within 4Å: Chain U: Q.189 Chain W: V.20, S.21 No protein-ligand interaction detected (PLIP)

6 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:V.44, 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: 1 interactions with chain H, 1 interactions with chain E Hydrogen bonds: H:A.54, 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: 1 interactions with chain P, 1 interactions with chain M Hydrogen bonds: P:E.52, 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:L.47, U:Q.48

6 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

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: AEIMQU
Genome polyprotein, capsid protein VP2: BFJNRV
Genome Polyprotein, vapsid protein VP3: CGKOSW
Genome Polyprotein, 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

Genome Polyprotein, capsid protein VP1

Genome polyprotein, capsid protein VP2

Genome Polyprotein, vapsid protein VP3

Genome Polyprotein, capsid protein VP4

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