SMTL ID : 4gbt.4 (5 other biounits)

Structural characterization of H-1 Parvovirus: comparison of infectious virions to replication defective particles

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-hexamer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: H.516, D.517 Chain E: Q.468 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.516, A:D.517, A:D.517 NA.3: 2 residues within 4Å: Chain B: H.516, D.517 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.516, B:D.517, B:D.517 NA.5: 2 residues within 4Å: Chain C: H.516, D.517 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.516, C:D.517, C:D.517 NA.7: 3 residues within 4Å: Chain A: Q.468 Chain D: H.516, D.517 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.516, D:D.517, A:Q.468 NA.9: 3 residues within 4Å: Chain D: Q.468 Chain E: H.516, D.517 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:Q.468, E:H.516, E:D.517 NA.11: 2 residues within 4Å: Chain F: H.516, D.517 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.516, F:D.517, F:D.517

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

CL.2: 2 residues within 4Å: Chain A: Q.290, T.414 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain B: Q.290, T.414 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain C: Q.290, T.414 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain D: Q.290, T.414 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain E: Q.290, T.414 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain F: Q.290, T.414 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halder, S. et al., Structural characterization of h-1 parvovirus: comparison of infectious virions to empty capsids. J.Virol. (2013)

Release Date

2013-02-27

Peptides

Capsid protein VP1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Capsid protein VP1

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