SMTL ID : 4v0q.1

Dengue Virus Full Length NS5 Complexed with SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: E.434, H.438, C.443, G.444, 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: 5 residues within 4Å: Chain B: E.434, H.438, C.443, G.444, 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 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.53, 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:V.129, A:D.143, A:D.143 Water bridges: A:R.81, A:S.85, A:G.103 pi-Stacking: A:H.107 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 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.53, 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:V.129, B:D.143, B:D.143 Water bridges: B:R.81, B:S.85, B:G.103 pi-Stacking: B:H.107

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: R.54, K.58, L.206 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.54, A:L.206 Hydrogen bonds: A:L.206 Salt bridges: A:K.58 ACT.5: 3 residues within 4Å: Chain A: R.35, K.39, R.54 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.39 Salt bridges: A:R.35 ACT.6: 4 residues within 4Å: Chain A: K.11, N.15, P.149, S.210 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.11, A:E.154 Salt bridges: A:K.11 ACT.7: 4 residues within 4Å: Chain A: H.49, V.684, R.685, I.688 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.684 Hydrogen bonds: A:I.688 Salt bridges: A:H.49 ACT.8: 5 residues within 4Å: Chain A: E.109, S.125 Chain B: S.519, K.665, H.698 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.109, A:S.125 Water bridges: B:K.665, B:K.665 Salt bridges: B:K.665, B:H.698 ACT.9: 2 residues within 4Å: Chain A: D.128, Y.131 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.126, A:D.128 ACT.14: 3 residues within 4Å: Chain B: R.54, K.58, L.206 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.54, B:L.206 Hydrogen bonds: B:L.206 Salt bridges: B:K.58 ACT.15: 3 residues within 4Å: Chain B: R.35, K.39, R.54 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.39 Salt bridges: B:R.35 ACT.16: 4 residues within 4Å: Chain B: K.11, N.15, P.149, S.210 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.11, B:E.154 Salt bridges: B:K.11 ACT.17: 4 residues within 4Å: Chain B: H.49, V.684, R.685, I.688 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.684 Hydrogen bonds: B:I.688 Salt bridges: B:H.49 ACT.18: 5 residues within 4Å: Chain A: S.519, K.665, H.698 Chain B: E.109, S.125 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.109, B:S.125 Water bridges: A:K.665, A:K.665 Salt bridges: A:K.665, A:H.698 ACT.19: 2 residues within 4Å: Chain B: D.128, Y.131 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.126, B:D.128

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 8 residues within 4Å: Chain A: Y.116, D.253, L.254, G.255, K.297, K.352, E.353, D.356 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.253, A:K.297, A:K.352, A:K.352, A:D.356 Water bridges: A:G.90 GOL.20: 8 residues within 4Å: Chain B: Y.116, D.253, L.254, G.255, K.297, K.352, E.353, D.356 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.253, B:K.297, B:K.352, B:K.352, B:D.356 Water bridges: B:G.90

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

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