SMTL ID : 6xpp.1

Crystal structure of itaconate modified Mycobaterium tuberculosis isocitrate lyase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

4 x ITN: 2-methylidenebutanedioic acid(Non-covalent)

ITN.1: 13 residues within 4Å: Chain A: W.93, D.108, D.153, C.191, G.192, H.193, R.228, E.285, N.313, S.315, S.317, T.347 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.93, A:T.347 Hydrogen bonds: A:G.192, A:E.285, A:N.313, A:S.315, A:S.317 Water bridges: A:G.92, A:K.189, A:R.228 Salt bridges: A:K.189, A:H.193, A:R.228 ITN.4: 13 residues within 4Å: Chain B: W.93, D.108, D.153, C.191, G.192, H.193, R.228, E.285, N.313, S.315, S.317, T.347 Ligands: MG.5 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.93, B:T.347 Hydrogen bonds: B:G.192, B:N.313, B:N.313, B:S.315, B:S.317, B:T.347 Water bridges: B:Y.89, B:G.92, B:K.189, B:R.228 Salt bridges: B:K.189, B:H.193, B:R.228 ITN.7: 13 residues within 4Å: Chain C: W.93, D.108, D.153, C.191, G.192, H.193, R.228, E.285, N.313, S.315, S.317, T.347 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.93, C:T.347 Hydrogen bonds: C:G.192, C:E.285, C:E.285, C:N.313, C:S.315, C:S.317 Water bridges: C:G.92, C:K.189, C:R.228 Salt bridges: C:K.189, C:H.193, C:R.228 ITN.10: 13 residues within 4Å: Chain D: W.93, D.108, D.153, C.191, G.192, H.193, R.228, E.285, N.313, S.315, S.317, T.347 Ligands: MG.11 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:W.93, D:T.347 Hydrogen bonds: D:G.192, D:E.285, D:N.313, D:N.313, D:S.315, D:S.317, D:T.347 Water bridges: D:Y.89, D:G.92, D:K.189, D:R.228 Salt bridges: D:K.189, D:H.193, D:R.228

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.108, D.153 Ligands: ITN.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.153, H2O.1, H2O.1, H2O.3 MG.3: 3 residues within 4Å: Chain A: A.276, A.279, Q.308 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.276, A:A.279, H2O.7, H2O.13, H2O.14 MG.5: 3 residues within 4Å: Chain B: D.108, D.153 Ligands: ITN.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.153, H2O.18, H2O.19, H2O.20 MG.6: 3 residues within 4Å: Chain B: A.276, A.279, Q.308 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.276, B:A.279, H2O.23, H2O.31, H2O.31 MG.8: 3 residues within 4Å: Chain C: D.108, D.153 Ligands: ITN.7 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.153, H2O.35, H2O.36, H2O.37 MG.9: 3 residues within 4Å: Chain C: A.276, A.279, Q.308 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.276, C:A.279, H2O.41, H2O.48, H2O.49 MG.11: 3 residues within 4Å: Chain D: D.108, D.153 Ligands: ITN.10 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.153, H2O.53, H2O.54, H2O.54 MG.12: 3 residues within 4Å: Chain D: A.276, A.279, Q.308 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:A.276, D:A.279, H2O.58, H2O.64, H2O.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwai, B.X.C. et al., Itaconate is a covalent inhibitor of the Mycobacterium tuberculosis isocitrate lyase. Rsc Med Chem (2021)

Release Date

2020-10-21

Peptides

Isocitrate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isocitrate lyase

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