SMTL ID : 6cj3.1

CRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM AND PYRUVATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.45, E.120, D.146 Ligands: PYR.5 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.120, A:D.146, H2O.1, H2O.1, PYR.5 MG.7: 4 residues within 4Å: Chain B: D.45, E.120, D.146 Ligands: PYR.11 5 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:E.120, B:D.146, H2O.7, H2O.7, PYR.11 MG.13: 4 residues within 4Å: Chain C: D.45, E.120, D.146 Ligands: PYR.17 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.120, C:D.146, H2O.12, H2O.12

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

ACT.2: 7 residues within 4Å: Chain A: R.158, R.164, D.165, V.166 Chain B: R.171, D.205, V.209 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.209 Water bridges: B:R.171, B:D.205, A:R.158, A:D.165 Hydrogen bonds: A:D.165, A:V.166 Salt bridges: A:R.158 ACT.3: 3 residues within 4Å: Chain A: R.28, A.32, P.219 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.32 Salt bridges: A:R.28 ACT.4: 4 residues within 4Å: Chain A: D.45, R.72 Chain B: D.261 Ligands: PYR.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.72 ACT.8: 7 residues within 4Å: Chain B: R.158, R.164, D.165, V.166 Chain C: R.171, D.205, V.209 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.209 Water bridges: C:R.171, C:D.205, B:R.158, B:D.165 Hydrogen bonds: B:D.165, B:V.166 Salt bridges: B:R.158 ACT.9: 3 residues within 4Å: Chain B: R.28, A.32, P.219 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.32 Salt bridges: B:R.28 ACT.10: 4 residues within 4Å: Chain B: D.45, R.72 Chain C: D.261 Ligands: PYR.11 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.72 ACT.14: 7 residues within 4Å: Chain A: R.171, D.205, V.209 Chain C: R.158, R.164, D.165, V.166 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:D.165, C:V.166 Water bridges: C:R.158, A:R.171, A:D.205, A:D.205 Salt bridges: C:R.158 Hydrophobic interactions: A:V.209 ACT.15: 3 residues within 4Å: Chain C: R.28, A.32, P.219 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.32 Salt bridges: C:R.28 ACT.16: 4 residues within 4Å: Chain A: D.261 Chain C: D.45, R.72 Ligands: PYR.17 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.72

6 x PYR: PYRUVIC ACID(Non-covalent)

PYR.5: 11 residues within 4Å: Chain A: R.72, L.118, E.120, M.141, G.143, A.144, E.145, D.146 Chain B: P.263 Ligands: MG.1, ACT.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.72, A:E.120, A:E.145, A:D.146 Water bridges: A:A.144 PYR.6: 6 residues within 4Å: Chain A: R.157, H.190, L.191, D.192, D.195 Chain B: Q.258 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.192 Hydrogen bonds: A:L.191, A:D.192 Water bridges: A:R.157 Salt bridges: A:R.157 PYR.11: 11 residues within 4Å: Chain B: R.72, L.118, E.120, M.141, G.143, A.144, E.145, D.146 Chain C: P.263 Ligands: MG.7, ACT.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.72, B:E.120, B:E.145, B:D.146 Water bridges: B:A.144 PYR.12: 6 residues within 4Å: Chain B: R.157, H.190, L.191, D.192, D.195 Chain C: Q.258 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.192 Hydrogen bonds: B:L.191, B:D.192 Water bridges: B:R.157 Salt bridges: B:R.157 PYR.17: 11 residues within 4Å: Chain A: P.263 Chain C: R.72, L.118, E.120, M.141, G.143, A.144, E.145, D.146 Ligands: MG.13, ACT.16 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.72, C:E.120, C:E.145, C:D.146 Water bridges: C:A.144 PYR.18: 6 residues within 4Å: Chain A: Q.258 Chain C: R.157, H.190, L.191, D.192, D.195 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:D.192 Hydrogen bonds: C:L.191, C:D.192 Water bridges: C:R.157 Salt bridges: C:R.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., An essential bifunctional enzyme inMycobacterium tuberculosisfor itaconate dissimilation and leucine catabolism. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2018-08-01

Peptides

Citrate lyase subunit beta-like protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Citrate lyase subunit beta-like protein

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