SMTL ID : 6as5.1

CRYSTAL STRUCTURE OF PROTEIN CitE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM, ACETOACETATE AND COENZYME A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.45, R.72, E.120, D.146 Ligands: AAE.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.120, A:D.146, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: D.45, E.120, D.146 Ligands: AAE.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.120, B:D.146, H2O.4, H2O.4 MG.10: 5 residues within 4Å: Chain C: D.45, K.100, E.120, D.146 Ligands: AAE.12 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.120, C:D.146, H2O.6, H2O.7

3 x COA: COENZYME A(Non-covalent)

COA.2: 14 residues within 4Å: Chain A: F.20, C.21, P.22, R.28, K.31, A.32, D.42, G.46, R.72, I.217, H.218, P.219 Chain C: A.252, M.259 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.22, C:A.252 Hydrogen bonds: A:F.20, A:R.28, A:R.28, A:I.217 Salt bridges: A:R.28, A:K.31, A:H.218 pi-Stacking: A:H.218 COA.7: 16 residues within 4Å: Chain A: A.252, F.253, M.259 Chain B: F.20, C.21, P.22, R.25, R.28, K.31, A.32, D.42, G.46, R.72, I.217, H.218, P.219 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.20, B:R.28, B:R.28, B:K.31, B:I.217 Salt bridges: B:R.28, B:K.31, B:H.218 pi-Cation interactions: B:R.28 Hydrophobic interactions: A:A.252 COA.11: 17 residues within 4Å: Chain B: A.252, M.259 Chain C: L.19, F.20, C.21, P.22, R.25, R.28, K.31, A.32, D.42, G.46, R.72, I.217, H.218, P.219 Ligands: AAE.12 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:F.20, C:R.28, C:I.217 Salt bridges: C:R.28, C:K.31, C:H.218 pi-Cation interactions: C:R.28 Hydrophobic interactions: B:A.252

3 x AAE: ACETOACETIC ACID(Non-functional Binders)

AAE.3: 11 residues within 4Å: Chain A: F.20, R.72, L.118, E.120, M.141, G.143, A.144, E.145, D.146, V.189 Ligands: MG.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.20, A:V.189 Hydrogen bonds: A:R.72, A:E.145, A:D.146, A:D.146 Water bridges: A:R.72, A:A.144 AAE.8: 10 residues within 4Å: Chain B: F.20, R.72, L.118, E.120, M.141, G.143, A.144, E.145, D.146 Ligands: MG.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.20, B:L.118 Hydrogen bonds: B:R.72, B:E.145, B:D.146 Water bridges: B:R.72 AAE.12: 11 residues within 4Å: Chain B: P.263 Chain C: F.20, R.72, L.118, E.120, G.143, A.144, E.145, D.146 Ligands: MG.10, COA.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.20 Hydrogen bonds: C:R.72, C:E.120, C:E.145, C:D.146, C:D.146 Water bridges: C:R.72, C:A.144

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

SO4.4: 5 residues within 4Å: Chain A: R.158, R.168 Chain B: R.168 Chain C: R.158, R.168 7 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 3 interactions with chain B Salt bridges: A:R.158, A:R.168, C:R.158, C:R.168, B:R.168 Hydrogen bonds: B:R.158, B:R.158 SO4.5: 4 residues within 4Å: Chain A: R.204, K.235 Chain B: A.159, R.164 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.159 Salt bridges: B:R.164, A:R.204, A:K.235 SO4.9: 3 residues within 4Å: Chain B: R.204 Chain C: A.159, R.164 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.159 Salt bridges: C:R.164, B:R.204

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain B: W.238, V.264, H.267 Chain C: E.145, S.155, S.156, R.157 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.155, C:S.156, C:R.157, B:H.267 Water bridges: C:S.156, C:R.157 GOL.14: 3 residues within 4Å: Chain C: E.234, W.238, R.241 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.234, C:E.234, C:R.241 Water bridges: C:W.238, C:W.238

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
B

C
C

Citrate lyase subunit beta-like protein

Related Entries With Identical Sequence