SMTL ID : 8f8k.1

The structure of Rv2173 from M. tuberculosis with IPP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: D.208, A.222, V.225, A.226, K.229, Q.268, K.295, R.296, T.297 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.222, A:K.229, A:K.229, A:V.298 Water bridges: A:D.208, A:E.212, A:Q.268, A:R.296 GOL.7: 4 residues within 4Å: Chain A: G.64, D.68, R.137, Y.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.64 GOL.12: 9 residues within 4Å: Chain B: D.208, A.222, V.225, A.226, K.229, Q.268, K.295, R.296, T.297 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.222, B:K.229, B:K.229, B:V.298 Water bridges: B:D.208, B:E.212, B:Q.268, B:R.296 GOL.18: 4 residues within 4Å: Chain B: G.64, D.68, R.137, Y.138 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.64

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: F.72, V.73, G.76, R.79, E.109 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.109 Hydrogen bonds: A:E.109 Salt bridges: A:R.79 ACT.3: 5 residues within 4Å: Chain A: R.124, S.125, A.126, Q.135, L.136 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.136 Hydrogen bonds: A:Q.135 Salt bridges: A:R.124 ACT.4: 5 residues within 4Å: Chain A: T.227, C.232, S.236, E.257, A.261 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.227, A:A.261 Hydrogen bonds: A:S.236 Salt bridges: A:R.237 ACT.6: 6 residues within 4Å: Chain A: R.81, K.229, T.230, Y.233, T.234 Ligands: IPE.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.81, A:T.234, A:T.234 Water bridges: A:D.271, A:D.271 ACT.13: 5 residues within 4Å: Chain B: F.72, V.73, G.76, R.79, E.109 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.109 Hydrogen bonds: B:E.109 Salt bridges: B:R.79 ACT.14: 5 residues within 4Å: Chain B: R.124, S.125, A.126, Q.135, L.136 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.136 Hydrogen bonds: B:Q.135 Salt bridges: B:R.124 ACT.15: 5 residues within 4Å: Chain B: T.227, C.232, S.236, E.257, A.261 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.227, B:A.261 Hydrogen bonds: B:S.236 Salt bridges: B:R.237 ACT.17: 6 residues within 4Å: Chain B: R.81, K.229, T.230, Y.233, T.234 Ligands: IPE.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.81, B:T.234, B:T.234 Water bridges: B:D.271, B:D.271

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

IPE.5: 14 residues within 4Å: Chain A: H.112, A.115, L.116, D.119, D.123, V.201, Q.205, K.229, Y.233, K.295 Ligands: ACT.6, CA.8, CA.9, CA.10 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:A.115, A:V.201, A:Q.205, A:K.229, A:Y.233 Water bridges: A:R.128, A:R.128, A:K.229, A:K.229, A:K.229, A:K.229, A:D.271, A:K.295, A:K.295, A:K.295 Salt bridges: A:K.229, A:K.229, A:K.295, A:K.295 IPE.16: 14 residues within 4Å: Chain B: H.112, A.115, L.116, D.119, D.123, V.201, Q.205, K.229, Y.233, K.295 Ligands: ACT.17, CA.19, CA.20, CA.21 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.115, B:V.201, B:Q.205, B:K.229, B:Y.233 Water bridges: B:R.128, B:R.128, B:K.229, B:K.229, B:K.229, B:K.229, B:D.271, B:K.295, B:K.295, B:K.295 Salt bridges: B:K.229, B:K.229, B:K.295, B:K.295

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.8: 4 residues within 4Å: Chain A: D.119, D.123 Ligands: IPE.5, CA.10 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.119, A:D.123, H2O.1, H2O.1, H2O.3 CA.9: 1 residues within 4Å: Ligands: IPE.5 No protein-ligand interaction detected (PLIP) CA.10: 4 residues within 4Å: Chain A: D.119, D.123 Ligands: IPE.5, CA.8 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.119, A:D.123, A:D.123, H2O.2, H2O.3 CA.19: 4 residues within 4Å: Chain B: D.119, D.123 Ligands: IPE.16, CA.21 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.119, B:D.123, H2O.4, H2O.5, H2O.6 CA.20: 1 residues within 4Å: Ligands: IPE.16 No protein-ligand interaction detected (PLIP) CA.21: 4 residues within 4Å: Chain B: D.119, D.123 Ligands: IPE.16, CA.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.119, B:D.123, B:D.123, H2O.6, H2O.7

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

CL.11: 2 residues within 4Å: Chain A: R.350, L.354 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: R.350, L.354 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Titterington, J.A. et al., Structures of Mycobacterium tuberculosis isoprenyl diphosphate synthase Rv2173 in substrate-bound forms. Acta Crystallogr.,Sect.F (2025)

Release Date

2023-11-29

Peptides

(2E,6E)-farnesyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

(2E,6E)-farnesyl diphosphate synthase

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