SMTL ID : 4g0r.3 (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

homo-hexamer

Ligands

24 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 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: Y.544, T.545, W.546, D.547 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: Y.347, K.350, K.528, Q.529 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: R.441, I.442, T.443 Chain G: W.253, P.356 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain C: R.441, T.456, D.460, R.461, F.462 Ligands: NA.15 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain C: Y.544, T.545, W.546, D.547 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: P.659 Chain C: Y.347, K.350, K.528, Q.529 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: R.441, I.442, T.443 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain E: R.441, T.456, D.460, R.461, F.462 Ligands: NA.25 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain E: Y.544, T.545, W.546, D.547 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain E: Y.347, K.350, K.528, Q.529 Chain G: P.659 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain E: R.441, I.442, T.443 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain G: R.441, T.456, D.460, R.461, F.462 Ligands: NA.35 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain G: Y.544, T.545, W.546, D.547 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain G: Y.347, K.350, K.528, Q.529 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain G: R.441, I.442, T.443 Chain I: W.253, P.356 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain I: R.441, T.456, D.460, R.461, F.462 Ligands: NA.45 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain I: Y.544, T.545, W.546, D.547 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain I: Y.347, K.350, K.528, Q.529 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain A: W.253, P.356 Chain I: R.441, I.442, T.443 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain K: R.441, T.456, D.460, R.461, F.462 Ligands: NA.55 Ligand excluded by PLIP EDO.52: 4 residues within 4Å: Chain K: Y.544, T.545, W.546, D.547 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain I: P.659 Chain K: Y.347, K.350, K.528, Q.529 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain K: R.441, I.442, T.443 Ligand excluded by PLIP

6 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 Protein-ligand interaction information (PLIP) not available DC.14: 6 residues within 4Å: Chain C: L.197, G.198, D.199, W.201, P.423, K.682 Protein-ligand interaction information (PLIP) not available DC.24: 6 residues within 4Å: Chain E: L.197, G.198, D.199, W.201, P.423, K.682 Protein-ligand interaction information (PLIP) not available DC.34: 6 residues within 4Å: Chain G: L.197, G.198, D.199, W.201, P.423, K.682 Protein-ligand interaction information (PLIP) not available DC.44: 6 residues within 4Å: Chain I: L.197, G.198, D.199, W.201, P.423, K.682 Protein-ligand interaction information (PLIP) not available DC.54: 6 residues within 4Å: Chain K: L.197, G.198, D.199, W.201, P.423, K.682 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:W.201, K:K.682 Hydrogen bonds: K:G.198, K:K.682 pi-Stacking: K:W.201

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

NA.5: 4 residues within 4Å: Chain A: P.440, R.441, R.461 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.441 NA.7: 5 residues within 4Å: Chain A: D.509, A.548, I.549, D.550 Chain G: R.497 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain G Hydrogen bonds: A:D.509, G:R.497 Water bridges: A:D.509 NA.15: 4 residues within 4Å: Chain C: P.440, R.441, R.461 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.441 Water bridges: C:R.441, C:T.456 NA.17: 4 residues within 4Å: Chain C: D.509, A.548, I.549, D.550 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.550 Water bridges: C:D.509 NA.25: 4 residues within 4Å: Chain E: P.440, R.441, R.461 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.441 Water bridges: E:R.441, E:T.456 NA.27: 4 residues within 4Å: Chain E: D.509, A.548, I.549, D.550 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.549 NA.35: 4 residues within 4Å: Chain G: P.440, R.441, R.461 Ligands: EDO.31 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.441 Water bridges: G:R.441, G:T.456 NA.37: 5 residues within 4Å: Chain G: D.509, A.548, I.549, D.550 Chain I: R.497 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain I Hydrogen bonds: G:I.549, I:R.497 Water bridges: G:D.509 NA.45: 4 residues within 4Å: Chain I: P.440, R.441, R.461 Ligands: EDO.41 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.441 NA.47: 5 residues within 4Å: Chain A: R.497 Chain I: D.509, A.548, I.549, D.550 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A Hydrogen bonds: I:D.550, A:R.497 NA.55: 4 residues within 4Å: Chain K: P.440, R.441, R.461 Ligands: EDO.51 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.441 Water bridges: K:R.441 NA.57: 4 residues within 4Å: Chain K: D.509, A.548, I.549, D.550 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:A.548

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

CL.8: 2 residues within 4Å: Chain A: H.516, D.517 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: H.516, D.517 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain E: H.516, D.517 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain G: H.516, D.517 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain I: H.516, D.517 Ligand excluded by PLIP CL.58: 2 residues within 4Å: Chain K: H.516, D.517 Ligand excluded by PLIP

12 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) MG.19: 5 residues within 4Å: Chain C: S.328 Chain D: C.1, G.3, T.7, A.9 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain C: N.329 Chain D: A.4, T.6, T.7, A.9 No protein-ligand interaction detected (PLIP) MG.29: 5 residues within 4Å: Chain E: S.328 Chain F: C.1, G.3, T.7, A.9 No protein-ligand interaction detected (PLIP) MG.30: 5 residues within 4Å: Chain E: N.329 Chain F: A.4, T.6, T.7, A.9 No protein-ligand interaction detected (PLIP) MG.39: 5 residues within 4Å: Chain G: S.328 Chain H: C.1, G.3, T.7, A.9 No protein-ligand interaction detected (PLIP) MG.40: 5 residues within 4Å: Chain G: N.329 Chain H: A.4, T.6, T.7, A.9 No protein-ligand interaction detected (PLIP) MG.49: 5 residues within 4Å: Chain I: S.328 Chain J: C.1, G.3, T.7, A.9 No protein-ligand interaction detected (PLIP) MG.50: 5 residues within 4Å: Chain I: N.329 Chain J: A.4, T.6, T.7, A.9 No protein-ligand interaction detected (PLIP) MG.59: 5 residues within 4Å: Chain K: S.328 Chain L: C.1, G.3, T.7, A.9 No protein-ligand interaction detected (PLIP) MG.60: 5 residues within 4Å: Chain K: N.329 Chain L: 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: ACEGIK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

Capsid protein VP1

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