SMTL ID : 6aq4.1

CRYSTAL STRUCTURE OF PROTEIN CiTE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM, PYRUVATE AND CITRAMALYL-COA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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: CQM.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: D.45, E.120, D.146 Ligands: CQM.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.120, B:D.146, H2O.8, H2O.8 MG.12: 4 residues within 4Å: Chain C: D.45, 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.13, H2O.14

2 x CQM: Citramalyl-CoA(Non-covalent)

CQM.2: 23 residues within 4Å: Chain A: L.19, F.20, C.21, P.22, R.28, K.31, A.32, D.42, R.72, L.118, E.120, G.143, A.144, E.145, D.146, I.217, H.218, P.219 Chain C: A.252, F.253, M.259, D.261 Ligands: MG.1 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:P.22, C:A.252 Hydrogen bonds: A:F.20, A:R.28, A:K.31, A:R.72, A:R.72, A:E.120, A:E.145, A:D.146, A:I.217, C:D.261 Water bridges: A:R.28, A:R.28, A:E.44, A:E.120, A:E.120 Salt bridges: A:R.28, A:K.31, A:H.218 pi-Cation interactions: A:R.28 CQM.9: 23 residues within 4Å: Chain A: A.252, F.253, M.259, D.261, P.263 Chain B: F.20, C.21, P.22, R.28, K.31, A.32, D.42, G.46, R.72, E.120, G.143, A.144, E.145, D.146, I.217, H.218, P.219 Ligands: MG.8 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.22, A:A.252 Hydrogen bonds: B:F.20, B:R.28, B:K.31, B:R.72, B:R.72, B:E.145, B:D.146, B:I.217, A:D.261 Water bridges: B:R.25, B:A.144, A:D.261 Salt bridges: B:R.28, B:K.31, B:H.218 pi-Cation interactions: B:R.28

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

PO4.3: 6 residues within 4Å: Chain A: R.158, R.168 Chain B: R.158, R.168 Chain C: R.158, R.168 8 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 3 interactions with chain C Water bridges: A:R.158, C:R.168 Salt bridges: A:R.158, A:R.168, B:R.168, C:R.168 Hydrogen bonds: B:R.158, C:R.158 PO4.4: 3 residues within 4Å: Chain B: D.165, R.168 Chain C: R.168 14 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C, 6 interactions with chain B Water bridges: A:D.165, A:H.169, A:H.169, C:R.168, C:H.169, C:H.169, B:H.169, B:H.169, B:H.169, B:H.169 Salt bridges: A:R.168, C:R.168, B:R.168 Hydrogen bonds: B:D.165 PO4.10: 5 residues within 4Å: Chain A: R.204, K.235 Chain B: R.158, A.159, R.164 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.159 Water bridges: B:S.155 Salt bridges: B:R.164, A:R.204, A:K.235

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: T.78, A.79, D.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.79, A:D.80, A:D.80, A:D.80 GOL.14: 6 residues within 4Å: Chain B: R.204, D.205, K.235 Chain C: R.158, A.159, R.164 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:A.159, C:R.164, C:R.164, B:R.204, B:K.235, B:K.235 Water bridges: B:D.205

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: R.204, P.231, S.232, K.235 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: E.49 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: E.49 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: I.108, A.134, D.135 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: P.63, T.91, A.92 Ligand excluded by PLIP

1 x PYR: PYRUVIC ACID(Non-covalent)

PYR.13: 10 residues within 4Å: Chain B: P.263 Chain C: R.72, L.118, E.120, G.143, A.144, E.145, D.146, V.189 Ligands: MG.12 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.189 Hydrogen bonds: C:R.72, C:E.145, C:D.146 Water bridges: C:R.72, C:A.144

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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