SMTL ID : 6chu.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 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: ACT.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.120, A:D.146, H2O.1, H2O.2, H2O.2 MG.7: 4 residues within 4Å: Chain B: D.45, E.120, D.146 Ligands: ACT.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.120, B:D.146, H2O.7, H2O.8, H2O.8 MG.13: 4 residues within 4Å: Chain C: D.45, E.120, D.146 Ligands: ACT.17 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.120, C:D.146, H2O.14, H2O.14, H2O.15

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

ACT.2: 7 residues within 4Å: Chain A: R.158, R.164, D.165, V.166 Chain C: R.171, D.205, V.209 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:V.209 Water bridges: C:R.171, A:R.158 Salt bridges: C:R.171, A:R.158 Hydrogen bonds: A:D.165, A:V.166 ACT.3: 3 residues within 4Å: Chain A: R.28, A.32, P.219 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.32, A:P.219 Salt bridges: A:R.28 ACT.4: 4 residues within 4Å: Chain A: D.45, R.72 Chain C: D.261 Ligands: ACT.5 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.261 Salt bridges: A:R.72 ACT.5: 8 residues within 4Å: Chain A: F.20, R.72, L.118, E.120, M.141, G.143 Ligands: MG.1, ACT.4 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Water bridges: C:D.261, A:E.145 Hydrophobic interactions: A:F.20 Salt bridges: A:R.72 ACT.8: 7 residues within 4Å: Chain A: R.171, D.205, V.209 Chain B: R.158, R.164, D.165, V.166 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.165, B:V.166 Water bridges: B:R.158, A:R.171 Salt bridges: B:R.158, A:R.171 Hydrophobic interactions: A:V.209 ACT.9: 3 residues within 4Å: Chain B: R.28, A.32, P.219 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.32, B:P.219 Salt bridges: B:R.28 ACT.10: 4 residues within 4Å: Chain A: D.261 Chain B: D.45, R.72 Ligands: ACT.11 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.72 Hydrogen bonds: A:D.261 ACT.11: 8 residues within 4Å: Chain B: F.20, R.72, L.118, E.120, M.141, G.143 Ligands: MG.7, ACT.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.20 Water bridges: B:E.145, A:D.261 Salt bridges: B:R.72 ACT.14: 7 residues within 4Å: Chain B: R.171, D.205, V.209 Chain C: R.158, R.164, D.165, V.166 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:V.209 Water bridges: B:R.171, C:R.158 Salt bridges: B:R.171, C:R.158 Hydrogen bonds: C:D.165, C:V.166 ACT.15: 3 residues within 4Å: Chain C: R.28, A.32, P.219 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.32, C:P.219 Salt bridges: C:R.28 ACT.16: 4 residues within 4Å: Chain B: D.261 Chain C: D.45, R.72 Ligands: ACT.17 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:R.72 Hydrogen bonds: B:D.261 ACT.17: 8 residues within 4Å: Chain C: F.20, R.72, L.118, E.120, M.141, G.143 Ligands: MG.13, ACT.16 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.20 Hydrogen bonds: C:D.146 Water bridges: C:E.145, B:D.261 Salt bridges: C:R.72

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

EDO.6: 5 residues within 4Å: Chain A: L.88, A.89, T.91, Y.93, R.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.91, A:R.113, A:R.113 EDO.12: 5 residues within 4Å: Chain B: L.88, A.89, T.91, Y.93, R.113 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.91, B:R.113, B:R.113 EDO.18: 5 residues within 4Å: Chain C: L.88, A.89, T.91, Y.93, R.113 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.91, C:R.113, C:R.113

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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