SMTL ID : 6arb.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 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.2 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.8: 4 residues within 4Å: Chain B: R.72, E.120, D.146 Ligands: PYR.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.120, B:D.146, H2O.6, H2O.8 MG.12: 3 residues within 4Å: Chain C: E.120, D.146 Ligands: PYR.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.120, C:D.146, H2O.12, H2O.13

3 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 8 residues within 4Å: Chain A: R.72, L.118, E.120, G.143, A.144, E.145, D.146 Ligands: MG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.72, A:E.145, A:D.146 Water bridges: A:R.72 PYR.9: 8 residues within 4Å: Chain A: P.263 Chain B: R.72, E.120, G.143, A.144, E.145, D.146 Ligands: MG.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.72, B:E.120, B:E.145, B:D.146 Water bridges: B:R.72, B:A.144 PYR.13: 9 residues within 4Å: Chain B: P.263 Chain C: R.72, L.118, E.120, G.143, A.144, E.145, D.146 Ligands: MG.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.72, C:E.145, C:D.146 Water bridges: C:R.72, C:A.144

3 x COA: COENZYME A(Non-covalent)

COA.3: 16 residues within 4Å: Chain A: F.20, C.21, P.22, R.25, R.28, A.32, D.42, G.46, R.72, I.217, H.218, P.219 Chain C: A.252, F.253, M.259, D.261 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:F.20, A:R.28, A:R.28, A:I.217, C:D.261, C:D.261 Water bridges: A:R.72 Salt bridges: A:R.28, A:H.218 pi-Stacking: A:H.218 Hydrophobic interactions: C:A.252 COA.10: 16 residues within 4Å: Chain A: A.252, M.259, D.261 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 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:A.252 Hydrogen bonds: A:D.261, A:D.261, B:F.20, B:R.28, B:R.28, B:I.217 Salt bridges: B:R.28, B:K.31, B:H.218 pi-Cation interactions: B:R.28 COA.14: 15 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, R.72, I.217, H.218, P.219 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:F.20, C:R.25, C:R.28, C:R.28, C:I.217 Water bridges: C:R.72 Salt bridges: C:R.28, C:K.31, C:H.218 pi-Cation interactions: C:R.28 Hydrophobic interactions: B:A.252

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 6 residues within 4Å: Chain A: R.158, R.168 Chain B: R.158, R.168 Chain C: R.158, R.168 7 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Water bridges: B:R.158 Salt bridges: B:R.158, B:R.168, A:R.158, A:R.168, C:R.158, C:R.168 PO4.5: 3 residues within 4Å: Chain A: G.77, T.78, A.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.79 Water bridges: A:D.80 PO4.15: 4 residues within 4Å: Chain C: R.230, H.233, L.236, R.240 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.240 Salt bridges: C:R.230, C:H.233, C:R.240

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: E.145, S.155, S.156, R.157 Chain C: W.238, V.264, H.267 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.156, A:R.157, C:H.267 Water bridges: A:E.145, A:S.156, A:R.157 GOL.7: 6 residues within 4Å: Chain A: R.204, D.205, K.235 Chain B: R.158, A.159, R.164 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:A.159, B:R.164, B:R.164, A:R.204, A:R.204, A:R.204, A:K.235, A:K.235 Water bridges: B:S.155, A:D.205 GOL.11: 8 residues within 4Å: Chain A: W.238, V.264, H.267 Chain B: E.145, S.154, S.155, S.156, R.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.156, B:S.156, B:R.157 GOL.16: 6 residues within 4Å: Chain B: H.267 Chain C: E.145, S.154, S.155, S.156, R.157 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.156, C:S.156, C:R.157 Water bridges: C:S.156, C:R.157 GOL.17: 6 residues within 4Å: Chain B: R.204, D.205, K.235 Chain C: R.158, A.159, R.164 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.159, C:R.164, C:R.164, B:K.235 Water bridges: B:D.205

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

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