SMTL ID : 8gll.3 (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

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

PEG.1: 10 residues within 4Å: Chain A: G.249, H.250, V.252, D.257, R.259, E.299, T.300, N.301, V.302, E.303 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.249, A:V.252, A:D.257, A:E.299, A:V.302, A:E.303 Water bridges: A:T.300

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

EDO.2: 1 residues within 4Å: Chain A: D.102 No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: R.161, H.162, P.273, F.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.161, A:R.161, A:H.162 EDO.4: 6 residues within 4Å: Chain A: K.27, D.28, R.251, V.252, Y.253, R.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.28, A:R.251 EDO.5: 6 residues within 4Å: Chain A: T.48, G.50, G.64, L.65, T.145, V.146 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.48, A:G.50, A:G.50, A:L.65, A:V.146 EDO.6: 5 residues within 4Å: Chain A: E.69, I.94, W.95, R.114 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.95, A:R.114 EDO.7: 7 residues within 4Å: Chain A: P.66, P.67, A.68, E.69, R.114, V.117, M.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.69, A:E.69, A:E.69 EDO.8: 7 residues within 4Å: Chain A: E.69, P.70, F.71, W.95, R.114 Ligands: EDO.6, EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.95, A:R.114 EDO.9: 2 residues within 4Å: Chain A: P.136, R.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.138, A:R.138 EDO.10: 3 residues within 4Å: Chain A: E.69, P.70 Ligands: EDO.8 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain A: E.268, G.271, A.272, Y.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.268, A:A.272 Water bridges: A:E.276 EDO.12: 5 residues within 4Å: Chain A: Q.125, R.128, A.134, V.135, R.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.135, A:R.153 EDO.16: 5 residues within 4Å: Chain A: P.10 Chain B: F.18, T.19, R.186, L.342 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.19, B:R.186 EDO.17: 5 residues within 4Å: Chain B: R.128, A.134, V.135, P.136, E.157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.133 EDO.18: 3 residues within 4Å: Chain B: H.250, R.251 Ligands: EDO.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.251 EDO.19: 4 residues within 4Å: Chain B: K.27, R.251, Y.253 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.251

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

SO4.13: 7 residues within 4Å: Chain A: H.176, N.179, H.211, G.213, R.259, F.324, R.328 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.179 Water bridges: A:R.259, A:R.259 Salt bridges: A:H.176, A:R.259, A:R.328 SO4.14: 5 residues within 4Å: Chain A: S.349, A.350 Chain B: P.25, G.177, M.178 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.178, A:A.350 Water bridges: B:K.27, A:R.347 SO4.15: 2 residues within 4Å: Chain A: G.249, H.250 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.250 SO4.20: 8 residues within 4Å: Chain A: R.347 Chain B: H.176, N.179, G.212, G.213, R.259, F.324, R.328 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.347, B:H.176, B:R.259, B:R.328 Hydrogen bonds: B:N.179 SO4.21: 5 residues within 4Å: Chain B: R.161, H.162, P.273, F.312, R.314 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.161, B:H.162, B:R.314

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
E

B
F

citrate synthase

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