SMTL ID : 9imr.1

Crystal structure of geranylgeranyl pyrophosphate synthase Rv0562 from Mycobacterium tuberculosis in complex with IPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

4 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.1: 14 residues within 4Å: Chain A: T.93, L.94, D.97, D.101, R.106, Q.158, K.182, Q.220, D.223, K.237 Ligands: IPE.2, MG.3, MG.4, MG.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.94, A:D.97 Hydrogen bonds: A:Q.220 Water bridges: A:D.97, A:D.101, A:D.101, A:D.101, A:D.101, A:R.106, A:Q.158, A:E.161, A:K.182, A:K.237, A:K.237, A:D.242 Salt bridges: A:R.106, A:K.182, A:K.237 IPE.2: 12 residues within 4Å: Chain A: G.56, K.57, R.60, H.90, L.94, R.106, R.107, T.183, F.219, Q.220, D.223 Ligands: IPE.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.94, A:T.183, A:F.219, A:D.223 Hydrogen bonds: A:K.57 Water bridges: A:K.57, A:K.57, A:K.57, A:R.58, A:R.58, A:R.60, A:R.60, A:R.106, A:R.106, A:R.333 Salt bridges: A:K.57, A:K.57, A:R.60, A:H.90, A:H.90, A:R.107 IPE.9: 14 residues within 4Å: Chain B: T.93, L.94, D.97, D.101, R.106, Q.158, K.182, Q.220, D.223, K.237 Ligands: IPE.10, MG.11, MG.12, MG.13 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.94, B:D.97 Hydrogen bonds: B:Q.220 Water bridges: B:D.101, B:R.106, B:R.106, B:E.161, B:E.161, B:K.182, B:D.223, B:K.237, B:K.237 Salt bridges: B:R.106, B:K.182, B:K.237 IPE.10: 13 residues within 4Å: Chain B: G.56, K.57, R.60, H.90, L.94, R.106, R.107, T.183, F.219, Q.220, D.223 Ligands: IPE.9, BCN.15 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.94, B:T.183, B:D.223 Hydrogen bonds: B:K.57 Water bridges: B:K.57, B:R.58, B:R.58, B:R.58, B:R.60, B:R.106, B:R.106, B:K.237, B:K.237 Salt bridges: B:K.57, B:K.57, B:R.60, B:H.90, B:H.90, B:R.107

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.97, D.101, E.161 Ligands: IPE.1, MG.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.97, A:D.101, H2O.2, H2O.4, H2O.6 MG.4: 4 residues within 4Å: Chain A: D.97, D.101 Ligands: IPE.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.97, A:D.101, H2O.9, H2O.9 MG.5: 4 residues within 4Å: Chain A: D.223, D.227, K.237 Ligands: IPE.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.223, H2O.3, H2O.3, H2O.4 MG.11: 4 residues within 4Å: Chain B: D.97, D.101 Ligands: IPE.9, MG.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.97, B:D.101, H2O.26, H2O.27 MG.12: 3 residues within 4Å: Chain B: D.223, D.227 Ligands: IPE.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.223, H2O.22, H2O.22, H2O.27 MG.13: 5 residues within 4Å: Chain B: D.97, D.101, E.161 Ligands: IPE.9, MG.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.97, B:D.101, H2O.21, H2O.23, H2O.27

4 x BCN: BICINE(Non-covalent)

BCN.6: 6 residues within 4Å: Chain A: G.117, N.118, N.119 Chain B: V.99, M.100, E.102 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.118, A:N.118, A:N.119, A:N.119, B:V.99 Water bridges: A:N.118, A:V.120, B:N.118 Salt bridges: B:E.102 BCN.7: 8 residues within 4Å: Chain A: R.288, A.289, S.290, P.291, M.293, A.294, K.297 Ligands: PEG.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.289, A:K.297 Water bridges: A:K.297, A:K.297 BCN.14: 6 residues within 4Å: Chain A: V.99, M.100, E.102 Chain B: G.117, N.118, N.119 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.118, B:N.118, B:N.119, B:N.119, A:V.99 Water bridges: B:V.120 Salt bridges: A:E.102 BCN.15: 9 residues within 4Å: Chain B: G.55, G.56, K.57, R.107, G.108, E.234, S.235, G.236 Ligands: IPE.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.56, B:K.57, B:K.57, B:K.57, B:R.107 Water bridges: B:A.54, B:R.107, B:R.107

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 2 residues within 4Å: Chain A: R.288 Ligands: BCN.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., Structural insight of a bi-functional isoprenyl diphosphate synthase Rv0562 from Mycobacterium tuberculosis. Int.J.Biol.Macromol. (2025)

Release Date

2025-07-09

Peptides

Nonaprenyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nonaprenyl diphosphate synthase

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