SMTL ID : 4kt8.1

The complex structure of Rv3378c-Y51FY90F with substrate, TPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: S.80, D.81, D.82, N.163, F.213, D.214 Chain B: S.220, G.221 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.80, A:N.163, A:D.214, B:G.221 Water bridges: A:D.81, A:D.82, A:D.82 PO4.2: 8 residues within 4Å: Chain A: G.221, K.222, T.223, S.224, R.251, H.252 Chain B: R.209, S.211 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.211, A:G.221, A:G.221 Salt bridges: B:R.209, A:R.251, A:H.252 PO4.3: 4 residues within 4Å: Chain A: P.216, L.217 Chain B: L.217 Ligands: PO4.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.217, A:L.217 PO4.5: 8 residues within 4Å: Chain A: S.220, G.221 Chain B: S.80, D.81, D.82, N.163, F.213, D.214 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.80, B:N.163, B:D.214, B:D.214, A:G.221 Water bridges: B:D.81 PO4.6: 8 residues within 4Å: Chain A: R.209, S.211 Chain B: G.221, K.222, T.223, S.224, R.251, H.252 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.211, B:G.221, B:G.221 Salt bridges: A:R.209, B:R.251, B:H.252 PO4.7: 4 residues within 4Å: Chain A: L.217 Chain B: P.216, L.217 Ligands: PO4.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.217, A:L.217

2 x 9AX: (2E)-3-methyl-5-[(1R,2S,8aS)-1,2,5,5-tetramethyl-1,2,3,5,6,7,8,8a-octahydronaphthalen-1-yl]pent-2-en-1-yl trihydrogen diphosphate(Non-covalent)

9AX.4: 16 residues within 4Å: Chain A: D.34, G.35, T.36, R.37, R.38, F.51, A.55, L.56, S.59, I.78, F.79, R.86, G.97, L.101, Y.233 Chain B: Y.259 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.51, A:F.51, A:A.55, A:F.79, A:L.101 Hydrogen bonds: A:G.35, A:T.36, A:R.37, A:R.38 Water bridges: A:R.38, A:R.38 Salt bridges: A:R.38, A:R.86 9AX.8: 16 residues within 4Å: Chain A: Y.259 Chain B: D.34, G.35, T.36, R.37, R.38, F.51, A.55, L.56, S.59, I.78, F.79, R.86, G.97, L.101, Y.233 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.51, B:F.51, B:A.55, B:F.79, B:L.101 Hydrogen bonds: B:G.35, B:T.36, B:R.37, B:R.38, A:Y.259 Water bridges: B:R.38, B:R.38 Salt bridges: B:R.38, B:R.86

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