SMTL ID : 3wqn.1

Crystal structure of Rv3378c_Y51F with TPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: D.82, N.164, F.214, D.215 Chain B: S.221, G.222 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.222, A:N.164 PO4.2: 8 residues within 4Å: Chain A: G.222, K.223, T.224, S.225, R.252, H.253 Chain B: R.210, S.212 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.222, A:G.222, B:S.212 Salt bridges: A:R.252, B:R.210 PO4.4: 6 residues within 4Å: Chain A: S.221, G.222 Chain B: D.82, N.164, F.214, D.215 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.222, B:N.164, B:D.215 PO4.5: 8 residues within 4Å: Chain A: R.210, S.212 Chain B: G.222, K.223, T.224, S.225, R.252, H.253 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.222, B:G.222, A:S.212 Salt bridges: B:R.252, A:R.210

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.3: 13 residues within 4Å: Chain A: F.34, G.36, T.37, R.38, R.39, A.56, L.57, S.60, I.79, F.80, Y.91, G.98, Y.234 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.34, A:T.37, A:R.38, A:A.56, A:F.80 Hydrogen bonds: A:G.36, A:T.37, A:R.38, A:R.39 Water bridges: A:R.39 Salt bridges: A:R.39 9AX.6: 13 residues within 4Å: Chain B: F.34, G.36, T.37, R.38, R.39, A.56, L.57, S.60, I.79, F.80, Y.91, G.98, Y.234 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.34, B:T.37, B:R.38, B:A.56, B:F.80 Hydrogen bonds: B:G.36, B:T.37, B:T.37, B:R.38, B:R.39 Water bridges: B:R.39 Salt bridges: B:R.39

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