SMTL ID : 6lkx.1

The structure of PRRSV helicase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.57, C.60, C.75, H.78 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.57, A:C.60, A:C.75, A:H.78 ZN.2: 4 residues within 4Å: Chain A: C.91, H.93, C.100, C.103 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.91, A:H.93, A:C.100, A:C.103 ZN.3: 5 residues within 4Å: Chain A: T.68, C.70, H.82, H.84, C.85 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.70, A:H.82, A:H.84, A:C.85 ZN.8: 4 residues within 4Å: Chain B: C.57, C.60, C.75, H.78 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.57, B:C.60, B:C.75, B:H.78 ZN.9: 5 residues within 4Å: Chain B: C.91, H.93, S.99, C.100, C.103 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.91, B:H.93, B:C.100, B:C.103 ZN.10: 4 residues within 4Å: Chain B: C.70, H.82, H.84, C.85 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.70, B:H.82, B:H.84, B:C.85

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: G.204, T.206, R.328, T.388, R.415 Chain B: R.484 Ligands: CIT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.328, A:R.415 GOL.6: 5 residues within 4Å: Chain A: G.364, F.389, D.390, V.391, D.476 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.390, A:D.390, A:V.391, A:V.391 GOL.7: 1 residues within 4Å: Chain A: E.493 No protein-ligand interaction detected (PLIP) GOL.13: 6 residues within 4Å: Chain B: H.356, D.422, L.427, Q.428, F.431, L.433 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.422, B:Q.428, B:F.431, B:L.433 GOL.14: 1 residues within 4Å: Chain B: G.437 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.455

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 13 residues within 4Å: Chain A: P.200, P.201, G.202, A.203, G.204, K.205, T.206, E.276, Q.302, R.328, G.386, R.413 Ligands: GOL.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.205, A:T.206 Hydrogen bonds: A:A.203, A:G.204, A:K.205, A:K.205, A:T.206, A:Q.302, A:G.386 Water bridges: A:K.205, A:Q.302 Salt bridges: A:K.205, A:R.328, A:R.328, A:R.413 CIT.11: 13 residues within 4Å: Chain B: P.200, P.201, G.202, A.203, G.204, K.205, T.206, E.276, Q.302, R.328, G.386, R.413 Ligands: CIT.12 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:A.203, B:G.204, B:K.205, B:K.205, B:K.205, B:T.206, B:T.206, B:Q.302, B:G.386 Salt bridges: B:K.205, B:R.328, B:R.328, B:R.413 CIT.12: 8 residues within 4Å: Chain A: R.484 Chain B: G.202, G.204, W.327, R.328, T.388, R.415 Ligands: CIT.11 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.204 Salt bridges: B:R.415, A:R.484, A:R.484 Water bridges: A:R.484

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Y. et al., Structural Characterization of the Helicase nsp10 Encoded by Porcine Reproductive and Respiratory Syndrome Virus. J.Virol. (2020)

Release Date

2020-05-27

Peptides

RNA-dependent RNA polymerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RNA-dependent RNA polymerase