SMTL ID : 3l28.1

Crystal structure of Zaire Ebola VP35 interferon inhibitory domain K339A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: Y.18, F.24, G.25, H.29, Q.33 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.18, A:G.25, A:Q.33 Salt bridges: A:H.29 SO4.2: 6 residues within 4Å: Chain A: S.55, E.58, D.60, Q.68, R.72 Chain B: R.111 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.68 Water bridges: A:S.55, A:E.58, A:R.72, B:R.111 Salt bridges: A:R.72, B:R.111 SO4.3: 4 residues within 4Å: Chain A: S.9, A.10, K.11, K.40 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.10, A:K.11 Water bridges: A:S.9 Salt bridges: A:K.40 SO4.8: 8 residues within 4Å: Chain B: L.21, P.22, G.23, F.24, G.25, T.26, H.29 Ligands: NA.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.23, B:F.24, B:G.25, B:T.26 Water bridges: B:H.29 SO4.9: 5 residues within 4Å: Chain A: E.58 Chain B: K.108, R.111 Chain E: P.82, V.83 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:V.83, E:V.83 Salt bridges: B:K.108, B:R.111 SO4.10: 4 residues within 4Å: Chain B: A.10, R.14, K.40 Ligands: NA.11 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.14, B:R.14, B:Q.33, B:K.40 Salt bridges: B:R.14, B:K.40 SO4.17: 8 residues within 4Å: Chain D: L.21, P.22, G.23, F.24, G.25, T.26, H.29 Ligands: NA.19 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.23, D:F.24, D:G.25, D:T.26 Water bridges: D:T.26, D:T.26 SO4.18: 3 residues within 4Å: Chain D: A.10, K.11, R.14 2 PLIP interactions: 2 interactions with chain D Water bridges: D:K.11 Salt bridges: D:R.14 SO4.22: 5 residues within 4Å: Chain E: S.55, E.58, D.60, Q.68 Chain F: R.111 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:D.60, E:Q.68 Water bridges: E:S.55, E:R.72, E:R.72, F:R.111, F:R.111 Salt bridges: F:R.111 SO4.25: 4 residues within 4Å: Chain F: S.106, K.108, R.111 Ligands: NA.23 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:K.108, F:R.111

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

CL.4: 2 residues within 4Å: Chain A: Q.63 Chain B: S.99 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.111 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: D.46, H.49 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: D.19, H.20 Chain B: R.101 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: S.9, A.10, K.40, L.45 Ligands: NA.11 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: R.111 Chain B: S.55, E.58, D.60, Q.68 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain C: R.111 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain D: S.106 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain D: R.111 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain E: Q.68, K.71 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain F: E.58, R.72 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain F: E.51, R.72, P.74 Ligand excluded by PLIP

5 x NA: SODIUM ION(Non-functional Binders)

NA.11: 4 residues within 4Å: Chain B: A.10, K.11 Ligands: SO4.10, CL.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.10, B:K.11 NA.12: 4 residues within 4Å: Chain B: P.22, T.26, Q.63 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.26, B:Q.63 NA.15: 6 residues within 4Å: Chain C: S.106, P.107, K.108, R.111, W.113 Chain D: G.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.108, C:W.113 NA.19: 6 residues within 4Å: Chain A: D.121 Chain D: Y.18, L.21, G.23, H.29 Ligands: SO4.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.121 NA.23: 4 residues within 4Å: Chain E: E.58 Chain F: S.106, R.111 Ligands: SO4.25 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.108, F:K.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leung, D.W. et al., Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-01-26

Peptides

Polymerase cofactor VP35: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Polymerase cofactor VP35