SMTL ID : 4rfu.1

Crystal structure of truncated P-domain from Grouper nervous necrosis virus capsid protein at 1.2A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-trimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.60, V.61, D.62 Chain C: D.60 Ligands: CA.5 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:D.60, A:D.60, A:V.61, A:D.62, H2O.15 CA.5: 5 residues within 4Å: Chain B: D.60, V.61 Chain C: D.60, D.62 Ligands: CA.1 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:D.60, C:D.62, B:D.60, B:V.61, H2O.15

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.70, F.72, R.84, F.95, T.96, D.97 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.70, A:R.84, A:F.95, A:D.97 Water bridges: A:D.97 GOL.3: 8 residues within 4Å: Chain A: N.17, D.18, Y.101, S.103, E.105, Q.106, P.107, R.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.101 Water bridges: A:S.103 GOL.6: 8 residues within 4Å: Chain B: N.17, D.18, Y.101, S.103, D.104, Q.106, P.107, R.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.101, B:D.104 Water bridges: B:S.103, B:S.103 GOL.7: 8 residues within 4Å: Chain C: N.17, Y.101, S.103, D.104, E.105, Q.106, P.107, R.108 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.101, C:Y.101, C:D.104 Water bridges: C:R.108, C:R.108

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: D.97, G.98, V.99 Chain C: P.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.97 Water bridges: A:Y.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, N.C. et al., Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection. Plos Pathog. (2015)

Release Date

2015-10-07

Peptides

Coat protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Coat protein