SMTL ID : 4ibg.1

Ebola virus VP35 bound to small molecule

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-dimer

Ligands

2 x 1D6: {4-[(2S)-2-(7-chloro-1,3-benzodioxol-5-yl)-4-hydroxy-3-(3-methylbenzoyl)-5-oxo-2,5-dihydro-1H-pyrrol-1-yl]phenyl}acetic acid(Non-covalent)

1D6.1: 18 residues within 4Å: Chain A: A.10, Q.30, Q.33, V.34, K.37, L.38, K.40, P.82, V.83, I.84, I.86, D.91, P.93, F.117 Chain B: H.85 Ligands: SO4.2, GOL.5, PO4.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.10, A:K.37, A:K.37, A:K.40, A:I.84, A:I.86, A:F.117 Hydrogen bonds: A:Q.30 Water bridges: A:K.11 Salt bridges: A:K.40 pi-Cation interactions: A:K.37 1D6.6: 18 residues within 4Å: Chain A: H.85 Chain B: A.10, Q.30, Q.33, V.34, K.37, L.38, K.40, P.82, V.83, I.84, I.86, D.91, P.93, F.117 Ligands: SO4.3, SO4.7, GOL.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.10, B:K.37, B:K.40, B:I.84, B:I.86, B:F.117 Hydrogen bonds: B:Q.30 Water bridges: B:A.10 Salt bridges: B:K.40 pi-Cation interactions: B:K.37

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

SO4.2: 9 residues within 4Å: Chain A: Y.18, G.25, T.26, H.29, Q.30, Q.33, P.93, C.96 Ligands: 1D6.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.26 Water bridges: A:Y.18, A:G.25, A:Q.33 SO4.3: 5 residues within 4Å: Chain A: H.85 Chain B: V.83, I.84, H.85 Ligands: 1D6.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.85 Hydrogen bonds: B:H.85, B:H.85 SO4.4: 3 residues within 4Å: Chain A: D.60, S.61, C.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.61, A:S.61 SO4.7: 8 residues within 4Å: Chain B: Y.18, G.25, T.26, H.29, Q.30, Q.33, P.93 Ligands: 1D6.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.30, B:Q.33 Water bridges: B:Y.18, B:G.25

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: P.82, V.83 Chain B: V.83, H.85, Q.118 Ligands: 1D6.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.85, A:V.83 GOL.8: 6 residues within 4Å: Chain A: V.83, H.85, Q.118 Chain B: P.82, V.83 Ligands: 1D6.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.83, A:H.85 GOL.9: 3 residues within 4Å: Chain B: D.60, S.61, C.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.60, B:S.61, B:S.61

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

PO4.10: 5 residues within 4Å: Chain A: V.83, I.84, H.85 Chain B: H.85 Ligands: 1D6.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.83, A:H.85 Salt bridges: B:H.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brown, C.S. et al., In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity. J.Mol.Biol. (2014)

Release Date

2014-03-19

Peptides

Polymerase cofactor VP35: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Polymerase cofactor VP35

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