SMTL ID : 4qpg.3 (3 other biounits)

Crystal structure of empty hepatitis A virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-6-6-6-mer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: R.146 Chain D: R.146 Ligands: CL.5 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: R.146 Chain D: R.146 Ligands: CL.6 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: R.146 Chain D: R.146 Ligands: CL.1 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: R.146 Chain D: R.146 Ligands: CL.2 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain G: R.146 Chain J: R.146 Ligands: CL.13 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain G: R.146 Chain J: R.146 Ligands: CL.14 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain G: R.146 Chain J: R.146 Ligands: CL.9 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain G: R.146 Chain J: R.146 Ligands: CL.10 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain M: R.146 Chain P: R.146 Ligands: CL.21 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain M: R.146 Chain P: R.146 Ligands: CL.22 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain M: R.146 Chain P: R.146 Ligands: CL.17 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain M: R.146 Chain P: R.146 Ligands: CL.18 Ligand excluded by PLIP

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: S.55, N.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.56 SO4.4: 1 residues within 4Å: Chain B: H.59 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.59 SO4.7: 2 residues within 4Å: Chain D: S.55, N.56 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.56 SO4.8: 1 residues within 4Å: Chain E: H.59 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:H.59 SO4.11: 2 residues within 4Å: Chain G: S.55, N.56 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.56 SO4.12: 1 residues within 4Å: Chain H: H.59 1 PLIP interactions: 1 interactions with chain H Salt bridges: H:H.59 SO4.15: 2 residues within 4Å: Chain J: S.55, N.56 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.56 SO4.16: 1 residues within 4Å: Chain K: H.59 1 PLIP interactions: 1 interactions with chain K Salt bridges: K:H.59 SO4.19: 2 residues within 4Å: Chain M: S.55, N.56 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:N.56 SO4.20: 1 residues within 4Å: Chain N: H.59 1 PLIP interactions: 1 interactions with chain N Salt bridges: N:H.59 SO4.23: 2 residues within 4Å: Chain P: S.55, N.56 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.56 SO4.24: 1 residues within 4Å: Chain Q: H.59 1 PLIP interactions: 1 interactions with chain Q Salt bridges: Q:H.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., Hepatitis A virus and the origins of picornaviruses. Nature (2015)

Release Date

2014-10-15

Peptides

Capsid protein VP1: ADGJMP
Capsid protein VP0: BEHKNQ
Capsid protein VP3: CFILOR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

M
A

P
A

B
B

E
B

H
B

K
B

N
B

Q
B

C
C

F
C

I
C

L
C

O
C

R
C

Capsid protein VP1

Capsid protein VP0

Capsid protein VP3

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