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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

monomer

Ligands

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

IOD.1: 2 residues within 4Å: Chain A: G.59 Ligands: SAH.13 Ligand excluded by PLIP IOD.2: 3 residues within 4Å: Chain A: G.149, E.150 Ligands: SAH.13 Ligand excluded by PLIP IOD.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.4: 1 residues within 4Å: Chain A: G.324 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: P.337 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: V.724, W.824 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: A.568, L.572 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: N.611 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: N.778, P.885 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: N.242 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: T.156, S.190 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: R.738 Ligand excluded by PLIP

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

SAH.13: 20 residues within 4Å: Chain A: S.57, G.59, G.82, C.83, G.84, G.86, G.87, W.88, T.105, K.106, H.111, E.112, V.131, D.132, V.133, F.134, D.147, I.148 Ligands: IOD.1, IOD.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.57, A:G.86, A:G.87, A:W.88, A:W.88, A:W.88, A:K.106, A:H.111, A:E.112, A:E.112, A:D.132, A:V.133 SAH.14: 3 residues within 4Å: Chain A: R.69, L.71, N.224 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.15: 4 residues within 4Å: Chain A: E.439, H.443, C.448, C.451 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.439, A:E.439, A:H.443, A:C.448, A:C.451 ZN.16: 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 4 residues within 4Å: Chain A: K.13, R.17, R.238, I.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.13, A:R.17, A:R.17, A:R.238 GOL.18: 6 residues within 4Å: Chain A: P.114, I.115, P.116, V.125, R.126, L.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.114, A:V.125, A:L.127

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
A

Genome polyprotein

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