- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.70 Å
- Oligo State
- homo-pentamer
- Ligands
- 20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 5 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
15 PLIP interactions:5 interactions with chain C, 5 interactions with chain A, 5 interactions with chain E- Hydrophobic interactions: C:W.201, C:K.682, A:W.201, A:K.682, E:W.201, E:K.682
- Hydrogen bonds: C:G.198, C:K.682, A:G.198, A:K.682, E:G.198, E:K.682
- pi-Stacking: C:W.201, A:W.201, E:W.201
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 availableDC.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 availableDC.34: 6 residues within 4Å:- Chain G: L.197, G.198, D.199, W.201, P.423, K.682
10 PLIP interactions:5 interactions with chain G, 5 interactions with chain I- Hydrophobic interactions: G:W.201, G:K.682, I:W.201, I:K.682
- Hydrogen bonds: G:G.198, G:K.682, I:G.198, I:K.682
- pi-Stacking: G:W.201, I:W.201
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- 10 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:D.509
- 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
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:R.441
NA.27: 4 residues within 4Å:- Chain E: D.509, A.548, I.549, D.550
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:I.549
- Water bridges: E:D.509
NA.35: 4 residues within 4Å:- Chain G: P.440, R.441, R.461
- Ligands: EDO.31
1 PLIP interactions:1 interactions with chain G- Hydrogen bonds: G:R.441
NA.37: 4 residues within 4Å:- Chain G: D.509, A.548, I.549, D.550
1 PLIP interactions:1 interactions with chain G- Hydrogen bonds: G:D.509
NA.45: 4 residues within 4Å:- Chain I: P.440, R.441, R.461
- Ligands: EDO.41
3 PLIP interactions:3 interactions with chain I- Hydrogen bonds: I:R.441
- Water bridges: I:R.441, I:T.456
NA.47: 4 residues within 4Å:- Chain I: D.509, A.548, I.549, D.550
2 PLIP interactions:2 interactions with chain I- Hydrogen bonds: I:D.550
- Water bridges: I:D.509
- 5 x CL: CHLORIDE ION(Non-functional Binders)
CL.8: 2 residues within 4Å:- Chain A: H.516, D.517
Ligand excluded by PLIPCL.18: 2 residues within 4Å:- Chain C: H.516, D.517
Ligand excluded by PLIPCL.28: 2 residues within 4Å:- Chain E: H.516, D.517
Ligand excluded by PLIPCL.38: 2 residues within 4Å:- Chain G: H.516, D.517
Ligand excluded by PLIPCL.48: 2 residues within 4Å:- Chain I: H.516, D.517
Ligand excluded by PLIP- 10 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)- 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: ACEGI
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
AE
AG
AI
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.70 Å
- Oligo State
- homo-pentamer
- Ligands
- 20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 5 x DC: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)
- 10 x NA: SODIUM ION(Non-functional Binders)
- 5 x CL: CHLORIDE ION(Non-functional Binders)
- 10 x MG: MAGNESIUM ION(Non-covalent)
- 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: ACEGI
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
AE
AG
AI
A