SMTL ID : 8gll.4 (3 other biounits)

R149E variant of Citrate Synthase (CitA) in Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: A.106, R.109, Q.110 No protein-ligand interaction detected (PLIP) EDO.2: 4 residues within 4Å: Chain A: R.128, W.154, Q.155 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.128, A:W.154 EDO.3: 4 residues within 4Å: Chain A: A.127, W.154, P.316 Ligands: EDO.2 No protein-ligand interaction detected (PLIP) EDO.4: 8 residues within 4Å: Chain A: A.17, F.18, T.19, R.186, E.338, L.342 Chain B: F.8, P.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.19, A:R.186 EDO.5: 3 residues within 4Å: Chain A: A.373 Chain B: R.46, R.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.373 EDO.7: 3 residues within 4Å: Chain B: S.233, G.237, R.241 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.241 EDO.8: 3 residues within 4Å: Chain B: E.69, W.95, R.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.114 Water bridges: B:E.69, B:E.69 EDO.9: 2 residues within 4Å: Chain B: G.249, H.250 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.250 EDO.10: 2 residues within 4Å: Chain B: S.63, R.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.63, B:R.109 EDO.12: 4 residues within 4Å: Chain B: E.276, V.279, A.280, Q.283 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.276, B:A.280, B:Q.283, B:Q.283 EDO.13: 6 residues within 4Å: Chain B: H.250, V.252, N.301, V.302, E.303 Ligands: EDO.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.250, B:V.302, B:E.303 Water bridges: B:N.301 EDO.14: 2 residues within 4Å: Chain B: R.251, V.252 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.252 Water bridges: B:R.251 EDO.15: 2 residues within 4Å: Chain B: G.354, G.356 No protein-ligand interaction detected (PLIP) EDO.16: 10 residues within 4Å: Chain B: G.249, H.250, R.251, V.252, D.257, E.299, T.300, N.301, V.302 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.249, B:D.257 Water bridges: B:V.252, B:T.300, B:N.301 EDO.17: 2 residues within 4Å: Chain B: D.102, D.104 No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 6 residues within 4Å: Chain A: H.176, N.179, G.213, R.259, F.324, R.328 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.179 Salt bridges: A:H.176, A:R.259, A:R.328 SO4.18: 8 residues within 4Å: Chain B: H.176, N.179, H.211, G.212, G.213, R.259, F.324, R.328 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.179, B:H.211, B:R.259 Water bridges: B:H.176 Salt bridges: B:H.176, B:H.211, B:R.328 SO4.19: 4 residues within 4Å: Chain B: R.161, H.162, P.273, F.312 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.312 Water bridges: B:R.314 Salt bridges: B:R.161, B:H.162

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

PEG.11: 4 residues within 4Å: Chain B: R.128, Q.132, W.154, Q.155 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.128, B:Q.132 Water bridges: B:R.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pathirage, R. et al., Mycobacterium tuberculosis CitA activity is modulated by cysteine oxidation and pyruvate binding. Rsc Med Chem (2023)

Release Date

2023-06-07

Peptides

citrate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

citrate synthase

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