SMTL ID : 6ime.1

Rv2361c complex with substrate analogues

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x GST: GERANYL S-THIOLODIPHOSPHATE(Non-covalent)

GST.1: 13 residues within 4Å: Chain A: M.75, D.76, G.77, N.78, G.79, R.80, R.89, H.93, Y.118, A.119, R.127 Chain B: R.292, F.293 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:D.76 Hydrogen bonds: A:D.76, A:G.77, A:G.79, A:R.80, A:R.89, A:R.89, B:F.293 Salt bridges: A:R.89, A:R.127, B:R.292 Water bridges: B:R.292 GST.8: 19 residues within 4Å: Chain A: A.296 Chain B: M.75, D.76, G.77, N.78, G.79, R.80, R.89, H.93, G.96, V.100, Y.118, A.119, R.127, F.138, Y.191, W.271 Ligands: MG.7, ISY.9 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.100, B:F.138 Hydrogen bonds: B:G.77, B:N.78, B:G.79, B:R.80, B:R.89, B:R.127, B:R.127 Water bridges: B:R.89, A:R.292, A:R.292, A:R.292, A:A.296 Salt bridges: B:R.80, B:R.89

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Y.261, F.293, G.294 Chain B: N.124 Ligands: ISY.9 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain B: D.76, R.80, R.127 Ligands: GST.8, ISY.9 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.76, H2O.17, H2O.19

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

CL.3: 3 residues within 4Å: Chain B: R.66, T.290, R.291 Ligand excluded by PLIP

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.4: 3 residues within 4Å: Chain B: W.125, R.165 Ligands: DTT.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.165, B:R.165

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.5: 7 residues within 4Å: Chain B: W.125, K.126, R.127, S.128, P.129, V.132 Ligands: CO3.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.127

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain B: A.64, L.67, P.68, N.69, G.111, I.112, K.113 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.111, B:K.113

1 x ISY: 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid(Non-covalent)

ISY.9: 18 residues within 4Å: Chain A: Y.261, R.292, F.293, G.294 Chain B: V.74, M.75, D.76, Y.118, A.119, F.120, N.124, R.127, R.244, R.250, S.252 Ligands: MG.2, MG.7, GST.8 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.74, B:Y.118, B:Y.118, B:Y.118 Hydrogen bonds: B:N.124, B:R.127, B:R.244, B:S.252, A:F.293, A:G.294 Water bridges: B:R.250, A:R.292, A:R.292, A:R.292, A:R.292 Salt bridges: B:R.244, B:R.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ko, T.-P. et al., Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase. Acta Crystallogr.,Sect.F (2019)

Release Date

2019-09-04

Peptides

Decaprenyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Decaprenyl diphosphate synthase