SMTL ID : 3wqm.1

Crystal structure of Rv3378c with inhibitor BPH-629

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x B29: [2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC ACID(Non-covalent)

B29.1: 13 residues within 4Å: Chain A: D.39, G.40, T.41, R.42, R.43, H.46, R.91, Y.95 Chain B: Y.264, S.265, L.272 Ligands: B29.2, MG.3 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.43, A:H.46, B:L.272 Hydrogen bonds: A:G.40, A:T.41, A:R.42, A:R.42, A:R.43, A:R.43, A:R.91 pi-Stacking: A:H.46, B:Y.264 B29.2: 15 residues within 4Å: Chain A: F.38, D.39, G.40, T.41, Y.56, Q.57, S.64, I.83, F.84, Y.95, Q.98, G.102, Y.238 Ligands: B29.1, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.38, A:Q.57, A:F.84, A:F.84 Hydrogen bonds: A:F.38, A:D.39, A:D.39, A:G.40, A:T.41, A:T.41, A:R.42, A:Y.56, A:Y.56, A:Y.95 pi-Stacking: A:Y.56, A:Y.95 B29.6: 13 residues within 4Å: Chain A: Y.264, S.265, L.272 Chain B: D.39, G.40, T.41, R.42, R.43, H.46, R.91, Y.95 Ligands: B29.7, MG.8 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.43, B:H.46, A:L.272 Hydrogen bonds: B:G.40, B:T.41, B:R.42, B:R.42, B:R.43, B:R.43, B:R.91, B:Y.95 pi-Stacking: B:H.46, A:Y.264 B29.7: 15 residues within 4Å: Chain B: F.38, D.39, G.40, T.41, Y.56, Q.57, S.64, I.83, F.84, Y.95, Q.98, G.102, Y.238 Ligands: B29.6, MG.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.38, B:Q.57, B:F.84, B:F.84 Hydrogen bonds: B:F.38, B:D.39, B:G.40, B:T.41, B:T.41, B:R.42, B:Y.56, B:Y.95 pi-Stacking: B:Y.56, B:Y.95

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.39, G.40 Ligands: B29.1, B29.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.39 MG.8: 4 residues within 4Å: Chain B: D.39, G.40 Ligands: B29.6, B29.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.39

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

PO4.4: 8 residues within 4Å: Chain A: G.226, K.227, T.228, S.229, R.256, H.257 Chain B: R.214, S.216 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.226, A:G.226 Salt bridges: A:R.256, A:H.257, B:R.214 Water bridges: B:S.216 PO4.5: 3 residues within 4Å: Chain A: K.12, E.13, D.16 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.10, A:S.10, A:K.12 PO4.9: 8 residues within 4Å: Chain A: R.214, S.216 Chain B: G.226, K.227, T.228, S.229, R.256, H.257 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.226, B:G.226 Salt bridges: B:R.256, B:H.257, A:R.214 Water bridges: A:S.216 PO4.10: 3 residues within 4Å: Chain B: K.12, E.13, D.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.16 Water bridges: B:S.10, B:S.10, B:K.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, H.C. et al., Structure and inhibition of tuberculosinol synthase and decaprenyl diphosphate synthase from Mycobacterium tuberculosis. J.Am.Chem.Soc. (2014)

Release Date

2014-02-26

Peptides

Diterpene synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Diterpene synthase