SMTL ID : 3l27.1

Crystal structure of Zaire Ebola VP35 interferon inhibitory domain R312A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 1 residues within 4Å: Chain A: G.25 Ligand excluded by PLIP CL.2: 6 residues within 4Å: Chain A: T.70, K.71, R.72, V.73, F.76, Q.77 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: P.6, I.8, S.9 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: S.9, A.10, K.40 Ligands: GOL.15 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: Q.118 Ligands: GOL.17 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: Y.18 Ligand excluded by PLIP

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: P.104, R.111, W.113, K.128 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.113 Salt bridges: A:K.128 PO4.4: 5 residues within 4Å: Chain A: Q.77, D.78, K.108, D.110, R.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.78 Water bridges: A:A.79 Salt bridges: A:R.111 PO4.5: 5 residues within 4Å: Chain A: R.72 Chain B: K.71, R.111 Ligands: GOL.16, GOL.17 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.72, B:K.71, B:K.128 Water bridges: B:K.128 PO4.14: 3 residues within 4Å: Chain B: I.16, H.20, Q.53 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.53, B:Q.53, B:Q.53 Salt bridges: B:H.20 PO4.19: 5 residues within 4Å: Chain C: F.76, Q.77, D.78, K.108, D.110 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.78, C:D.78, C:D.110, C:D.110 Water bridges: C:A.79 Salt bridges: C:K.108 PO4.23: 3 residues within 4Å: Chain D: I.16, H.20, Q.53 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.53, D:Q.53, D:Q.53 Salt bridges: D:H.20 PO4.24: 5 residues within 4Å: Chain D: Q.77, D.78, K.108, D.110, R.111 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.78, D:D.78, D:D.78 Water bridges: D:A.79 PO4.25: 4 residues within 4Å: Chain B: I.47 Chain D: R.111, W.113, K.128 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Water bridges: D:R.111, D:W.113, D:K.128, B:R.72, B:R.72 Salt bridges: D:R.111, D:K.128 PO4.26: 1 residues within 4Å: Ligands: GOL.28 No protein-ligand interaction detected (PLIP)

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: K.71, D.110, R.111 Ligands: PO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.71, A:D.110, A:R.111 GOL.7: 6 residues within 4Å: Chain A: I.16, H.20, F.52, Q.53, L.56 Chain B: K.98 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.53, B:K.98 GOL.8: 4 residues within 4Å: Chain A: S.9, A.10, K.11, K.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.9, A:S.9 Water bridges: A:A.10 GOL.15: 5 residues within 4Å: Chain B: S.9, A.10, K.11, K.40 Ligands: CL.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.9, B:A.10, B:K.11 GOL.16: 8 residues within 4Å: Chain A: R.72 Chain B: I.67, K.71, D.110, R.111, G.112, I.129 Ligands: PO4.5 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.72, B:K.71, B:D.110 Water bridges: A:E.58, A:R.72, B:I.109, B:G.112 GOL.17: 6 residues within 4Å: Chain B: P.104, R.111, W.113, K.128 Ligands: PO4.5, CL.12 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:R.72, B:K.128 Hydrogen bonds: B:K.128 GOL.20: 5 residues within 4Å: Chain C: S.9, A.10, K.11, R.14, K.40 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.10, C:K.11, C:R.14, C:R.14 Water bridges: C:S.9, C:S.9 GOL.21: 5 residues within 4Å: Chain B: K.108, R.111 Chain C: P.82, V.83, H.85 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.108, B:K.108, B:R.111, C:V.83 GOL.27: 4 residues within 4Å: Chain D: S.9, A.10, K.11, K.40 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.10, D:K.11, D:K.40 Water bridges: D:S.9, D:S.9 GOL.28: 2 residues within 4Å: Chain D: R.72 Ligands: PO4.26 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.72 Water bridges: D:E.51, D:E.51

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

NA.9: 5 residues within 4Å: Chain B: P.74, I.75, Q.77 Chain C: I.75, Q.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.75

2 x K: POTASSIUM ION(Non-covalent)

K.18: 3 residues within 4Å: Chain C: L.21, P.22, G.23 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:L.21, C:G.23 K.22: 3 residues within 4Å: Chain D: L.21, P.22, G.23 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.21, D:G.23, H2O.10

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Polymerase cofactor VP35