SMTL ID : 4v0r.1

DENGUE VIRUS FULL LENGTH NS5 COMPLEXED WITH GTP AND SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: E.434, H.438, C.443, C.446 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.434, A:H.438, A:C.443, A:C.446 ZN.2: 4 residues within 4Å: Chain A: H.709, H.711, C.725, C.844 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.709, A:C.725, A:C.844 ZN.11: 4 residues within 4Å: Chain B: E.434, H.438, C.443, C.446 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.434, B:H.438, B:C.443, B:C.446 ZN.12: 4 residues within 4Å: Chain B: H.709, H.711, C.725, C.844 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.709, B:C.725, B:C.844

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

SAH.3: 18 residues within 4Å: Chain A: S.53, G.55, G.78, C.79, G.80, G.82, G.83, W.84, T.101, K.102, H.107, E.108, K.127, D.128, V.129, F.130, D.143, I.144 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.53, A:G.78, A:G.82, A:G.83, A:W.84, A:W.84, A:K.102, A:H.107, A:E.108, A:E.108, A:E.108, A:D.128, A:D.128, A:V.129, A:D.143 Water bridges: A:R.81 SAH.13: 18 residues within 4Å: Chain B: S.53, G.55, G.78, C.79, G.80, G.82, G.83, W.84, T.101, K.102, H.107, E.108, K.127, D.128, V.129, F.130, D.143, I.144 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.53, B:G.78, B:G.82, B:G.83, B:W.84, B:W.84, B:K.102, B:H.107, B:E.108, B:E.108, B:E.108, B:D.128, B:D.128, B:V.129, B:D.143 Water bridges: B:R.81

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.4: 14 residues within 4Å: Chain A: K.11, L.14, N.15, L.17, R.19, F.22, K.26, S.147, S.148, P.149, E.154, R.208, S.210 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.11, A:L.17, A:L.17, A:R.19, A:S.147, A:E.154, A:S.210 Water bridges: A:R.19, A:R.19, A:R.208, A:R.208 Salt bridges: A:K.26, A:K.26, A:R.208, A:R.208 pi-Stacking: A:F.22, A:F.22 GTP.14: 14 residues within 4Å: Chain B: K.11, L.14, N.15, L.17, R.19, F.22, K.26, S.147, S.148, P.149, E.154, R.208, S.210 Ligands: MG.16 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.11, B:L.17, B:L.17, B:R.19, B:S.147, B:E.154, B:S.210 Water bridges: B:R.19, B:R.19, B:R.208, B:R.208 Salt bridges: B:K.26, B:K.26, B:R.208, B:R.208 pi-Stacking: B:F.22, B:F.22

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 2 residues within 4Å: Chain A: D.530, D.661 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.530, A:D.661, H2O.12, H2O.12, H2O.13, H2O.15 MG.6: 1 residues within 4Å: Ligands: GTP.4 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain B: D.530, D.661 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.530, B:D.661, H2O.28, H2O.28, H2O.28, H2O.30 MG.16: 1 residues within 4Å: Ligands: GTP.14 No protein-ligand interaction detected (PLIP)

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 3 residues within 4Å: Chain A: P.360, R.537, Q.690 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.537, A:Q.690 Water bridges: A:R.537 FMT.8: 2 residues within 4Å: Chain A: H.49, R.685 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.49 FMT.9: 4 residues within 4Å: Chain A: R.35, K.39, R.54, R.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.35, A:R.81 FMT.17: 3 residues within 4Å: Chain B: P.360, R.537, Q.690 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.537, B:Q.690 Water bridges: B:R.537 FMT.18: 2 residues within 4Å: Chain B: H.49, R.685 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.49 FMT.19: 4 residues within 4Å: Chain B: R.35, K.39, R.54, R.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.35, B:R.81

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: Y.116, D.253, L.254, K.297, K.352, D.356, T.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.253, A:K.297, A:K.352 GOL.20: 7 residues within 4Å: Chain B: Y.116, D.253, L.254, K.297, K.352, D.356, T.357 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.253, B:K.297, B:K.352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., A Crystal Structure of the Dengue Virus Ns5 Protein Reveals a Novel Inter-Domain Interface Essential for Protein Flexibility and Virus Replication. Plos Pathog. (2015)

Release Date

2015-01-28

Peptides

NS5 POLYMERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NS5 POLYMERASE