SMTL ID : 4g0r.1 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: R.441, T.456, D.460, R.461, F.462 Ligands: NA.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.441, A:T.456, A:F.462 Water bridges: A:T.456 EDO.2: 4 residues within 4Å: Chain A: Y.544, T.545, W.546, D.547 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.544, A:T.545, A:D.547 EDO.3: 4 residues within 4Å: Chain A: Y.347, K.350, K.528, Q.529 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.528 Water bridges: A:K.350, A:K.350 EDO.6: 3 residues within 4Å: Chain A: R.441, I.442, T.443 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.443

1 x DC: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DC.4: 6 residues within 4Å: Chain A: L.197, G.198, D.199, W.201, P.423, K.682 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.201, A:K.682 Hydrogen bonds: A:G.198, A:K.682 pi-Stacking: A:W.201

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

NA.5: 4 residues within 4Å: Chain A: P.440, R.441, R.461 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.441 Water bridges: A:R.441 NA.7: 4 residues within 4Å: Chain A: D.509, A.548, I.549, D.550 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.549 Water bridges: A:D.509

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

CL.8: 2 residues within 4Å: Chain A: H.516, D.517 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 5 residues within 4Å: Chain A: S.328 Chain B: C.1, G.3, T.7, A.9 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain A: N.329 Chain B: A.4, T.6, T.7, A.9 No protein-ligand interaction detected (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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Capsid protein VP1

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