SMTL ID : 6kr3.2 (1 other biounit)

Crystal structure of Dengue virus nonstructural protein NS5 (form 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

monomer

Ligands

3 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 1 residues within 4Å: Chain A: G.59 Ligand excluded by PLIP IOD.2: 1 residues within 4Å: Chain A: A.568 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: N.611, G.663, D.664 Ligand excluded by PLIP

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 2 residues within 4Å: Chain A: R.69, L.71 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.69, A:L.71 Hydrogen bonds: A:R.69 SAH.5: 17 residues within 4Å: Chain A: S.57, D.80, G.82, C.83, G.84, G.87, W.88, T.105, K.106, H.111, E.112, V.131, D.132, V.133, F.134, D.147, I.148 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.147 Hydrogen bonds: A:S.57, A:G.82, A:G.87, A:W.88, A:K.106, A:E.112, A:D.132, A:V.133, A:D.147, A:D.147

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: E.439, H.443, C.448, C.451, T.573 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.439, A:H.443, A:C.448, A:C.451 ZN.7: 4 residues within 4Å: Chain A: H.713, H.715, C.729, C.848 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.713, A:H.715, A:C.729, A:C.848

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: D.334, I.335, P.337, T.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.340 GOL.9: 1 residues within 4Å: Chain A: M.344 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain A: K.331, P.332, S.856, T.859, W.860 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.856

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, J. et al., A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase. Plos Pathog. (2020)

Release Date

2020-04-01

Peptides

Genome polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Genome polyprotein

Related Entries With Identical Sequence