SMTL ID : 8gmk.1

Pyruvate bound structure of Citrate Synthase (CitA) in Mycobacterium Tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 10 residues within 4Å: Chain A: P.67, A.68, V.117, L.120, S.121, I.140, V.146, R.149, F.150, R.153 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.120, A:V.146, A:F.150 Hydrogen bonds: A:A.68 Water bridges: A:R.149, A:R.149 Salt bridges: A:R.149, A:R.153 PYR.15: 10 residues within 4Å: Chain B: P.67, A.68, V.117, L.120, S.121, I.140, V.146, R.149, F.150, R.153 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.117, B:L.120, B:V.146, B:F.150 Hydrogen bonds: B:A.68 Water bridges: B:R.149, B:R.153 Salt bridges: B:R.149, B:R.153

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 2 residues within 4Å: Chain A: A.127, R.128 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.132

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

EDO.3: 1 residues within 4Å: Chain A: Q.155 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: D.311, R.314 Ligands: PEG.10 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: E.256, R.264, E.282, L.286 Ligand excluded by PLIP EDO.6: 1 residues within 4Å: Chain A: A.255 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: A.272, P.273, R.274, V.308, D.311, F.312 Ligands: PEG.10 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: G.212, G.213, N.301, E.303 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: D.79 Chain B: A.92, P.93 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: H.76, G.129, I.130 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: R.347 Chain B: D.13 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: T.48, G.50, D.51, G.64, L.65, T.145, V.146 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: A.134, V.135, P.136 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain B: H.176, N.179, H.211, G.212, G.213, R.259, F.324, R.328 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: T.19, E.21, E.338, L.342 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: P.273, R.274, D.311, F.312 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain B: E.21, R.35 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: W.366, E.367, V.369, T.371 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: S.63, G.64, P.66, P.67 Ligand excluded by PLIP

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

PEG.8: 9 residues within 4Å: Chain A: G.64, L.65, P.66, P.67, C.143, S.144, T.145, V.146, R.149 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.64, A:R.149, A:R.149 Water bridges: A:V.146 PEG.10: 9 residues within 4Å: Chain A: R.161, H.162, P.273, R.274, D.311, F.312, R.314 Ligands: EDO.4, EDO.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.161, A:H.162, A:R.274 Water bridges: A:R.161, A:R.274 PEG.12: 2 residues within 4Å: Chain A: G.29, G.30 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.261 PEG.22: 3 residues within 4Å: Chain B: D.58, S.63, R.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.58, B:S.63 Water bridges: B:R.109 PEG.25: 8 residues within 4Å: Chain B: D.79, R.81, S.207, N.318, M.319, M.320, P.321, A.322 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.81, B:R.81, B:M.319, B:A.322 Water bridges: B:V.80

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
A

B
B

citrate synthase

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