SMTL ID : 8f8l.1

The structure of Rv2173 from M. tuberculosis with DMAP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.1: 10 residues within 4Å: Chain A: H.112, D.119, D.123, R.128, V.201, Q.205, K.285, K.295 Ligands: CA.3, CA.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.201, A:Q.205 Water bridges: A:D.119, A:S.125, A:S.125, A:S.125, A:R.128, A:D.208 Salt bridges: A:R.128, A:K.229, A:K.285, A:K.295 DMA.5: 10 residues within 4Å: Chain B: H.112, D.119, D.123, R.128, V.201, Q.205, K.285, K.295 Ligands: CA.7, CA.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.201, B:Q.205 Water bridges: B:D.119, B:S.125, B:S.125, B:S.125, B:R.128, B:D.208 Salt bridges: B:R.128, B:K.229, B:K.285, B:K.295

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: G.64, L.65, R.137, Y.138, L.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.137 Water bridges: A:D.61, A:G.64, A:L.141 GOL.6: 5 residues within 4Å: Chain B: G.64, L.65, R.137, Y.138, L.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.137 Water bridges: B:D.61, B:G.64, B:L.141

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.119, D.123, K.229 Ligands: DMA.1, CA.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.119, A:D.123, A:D.123, H2O.5, H2O.5 CA.4: 4 residues within 4Å: Chain A: D.119, D.123 Ligands: DMA.1, CA.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.119, A:D.123, H2O.1, H2O.5 CA.7: 5 residues within 4Å: Chain B: D.119, D.123, K.229 Ligands: DMA.5, CA.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.119, B:D.123, B:D.123, H2O.10, H2O.10 CA.8: 4 residues within 4Å: Chain B: D.119, D.123 Ligands: DMA.5, CA.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.119, B:D.123, H2O.6, H2O.10

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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