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

Viral helicase protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x U- U- U- U- U- A- A- U: RNA (5'-R(P*UP*UP*UP*UP*UP)-3')(Non-covalent)

U-U-U-U-U-A-A-U.1: 29 residues within 4Å: Chain A: E.95, Y.132, P.159, Y.161, F.164, G.209, K.210, K.211, T.233, D.235, S.236, L.239, N.240, G.285, F.286, F.287, C.359, F.360, R.361, G.362, W.363, K.365, T.378, A.380, N.400, P.401, L.402, H.409 Ligands: GOL.19 Protein-ligand interaction information (PLIP) not available

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 18 residues within 4Å: Chain A: P.188, G.189, S.190, G.191, K.192, S.193, A.194, R.311, R.312, G.384, T.386, W.450 Ligands: MG.3, AL.4, F.5, F.6, F.7, F.8 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.189, A:S.190, A:G.191, A:K.192, A:S.193, A:A.194, A:R.311, A:T.386, A:T.386 Water bridges: A:S.193, A:K.197, A:D.252, A:R.312, A:R.312, A:R.416 Salt bridges: A:K.192, A:K.197, A:R.312, A:R.312

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: S.193, D.252, E.253 Ligands: ADP.2, AL.4, F.5, F.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.193, H2O.1, H2O.1, H2O.1

1 x AL: ALUMINUM ION(Non-covalent)

AL.4: 11 residues within 4Å: Chain A: G.189, E.253, Q.283, R.312, R.416 Ligands: ADP.2, MG.3, F.5, F.6, F.7, F.8 No protein-ligand interaction detected (PLIP)

4 x F: FLUORIDE ION(Non-covalent)

F.5: 9 residues within 4Å: Chain A: R.312, G.384, R.416 Ligands: ADP.2, MG.3, AL.4, F.6, F.7, F.8 No protein-ligand interaction detected (PLIP) F.6: 8 residues within 4Å: Chain A: P.188, K.192, Q.283 Ligands: ADP.2, AL.4, F.5, F.7, F.8 No protein-ligand interaction detected (PLIP) F.7: 9 residues within 4Å: Chain A: S.193, E.253, G.384 Ligands: ADP.2, MG.3, AL.4, F.5, F.6, F.8 No protein-ligand interaction detected (PLIP) F.8: 10 residues within 4Å: Chain A: P.188, G.189, Q.283, R.312, R.416 Ligands: ADP.2, AL.4, F.5, F.6, F.7 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 1 residues within 4Å: Chain A: N.337 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: K.282, L.324, H.325 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: R.311, T.333 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 8 residues within 4Å: Chain A: R.140, C.141, C.142, K.143, E.146, F.164, E.167 Ligands: GOL.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.140, A:R.140, A:E.146 GOL.13: 8 residues within 4Å: Chain A: S.88, V.92, A.165, R.172, D.235, L.238, L.239, T.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.88, A:R.172 Water bridges: A:A.165 GOL.14: 8 residues within 4Å: Chain A: D.81, P.176, Y.177, K.178, I.179, V.181, L.263, I.266 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.81, A:I.179, A:I.179 Water bridges: A:S.78, A:Y.177 GOL.15: 9 residues within 4Å: Chain A: F.255, C.257, S.259, L.262, N.297, H.298, N.299, I.300, C.301 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.257, A:N.297, A:N.299, A:I.300, A:C.301 GOL.16: 5 residues within 4Å: Chain A: L.205, S.230, R.232, N.243, R.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.230, A:N.243, A:R.244 GOL.17: 4 residues within 4Å: Chain A: R.202, I.229, S.230, R.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.202, A:S.230 Water bridges: A:D.204, A:R.244 GOL.18: 3 residues within 4Å: Chain A: G.8, A.9, S.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.8 GOL.19: 7 residues within 4Å: Chain A: Y.132, F.164, L.239, N.240 Ligands: U-U-U-U-U-A-A-U.1, U-U-U-U-U-A-A-U.1, GOL.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.132, A:Y.132, A:N.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Law, Y.S. et al., Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-04-10

Peptides

helicase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

helicase

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