SMTL ID : 6c4c.1 (1 other biounit)

Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with glyoxylate and pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

2 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.1: 14 residues within 4Å: Chain A: Y.103, S.105, G.106, W.107, D.122, D.167, H.194, X.205, R.242, W.297, F.359, T.361, L.362 Ligands: MG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.105, A:G.106, A:W.107, A:R.242 Water bridges: A:K.203, A:K.203 GLV.10: 13 residues within 4Å: Chain D: Y.103, S.105, G.106, W.107, D.122, D.167, H.194, X.205, R.242, W.297, T.361, L.362 Ligands: MG.11 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.105, D:G.106, D:W.107, D:R.242 Water bridges: D:K.203, D:K.203

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 10 residues within 4Å: Chain A: G.106, W.107, D.122, D.167, E.169, H.194, K.203, X.205, R.242 Ligands: GLV.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.167, H2O.1, H2O.1, H2O.3 MG.3: 3 residues within 4Å: Chain A: A.290, A.293, Q.322 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.290, A:A.293, H2O.3, H2O.8, H2O.9 MG.5: 10 residues within 4Å: Chain B: G.106, W.107, D.122, D.167, E.169, H.194, K.203, X.205, R.242 Ligands: PYR.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.167, H2O.10, H2O.10, H2O.12 MG.6: 5 residues within 4Å: Chain B: D.39, A.290, P.291, A.293, Q.322 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.290, B:A.293, H2O.12, H2O.17, H2O.17 MG.8: 10 residues within 4Å: Chain C: G.106, W.107, D.122, D.167, E.169, H.194, K.203, X.205, R.242 Ligands: PYR.7 5 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: C:D.167, PYR.7, H2O.18, H2O.19, H2O.19 MG.9: 4 residues within 4Å: Chain C: A.290, P.291, A.293, Q.322 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.290, C:A.293, H2O.19, H2O.24, H2O.24 MG.11: 10 residues within 4Å: Chain D: G.106, W.107, D.122, D.167, E.169, H.194, K.203, X.205, R.242 Ligands: GLV.10 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.167, H2O.25, H2O.26, H2O.27 MG.12: 5 residues within 4Å: Chain D: D.39, A.290, P.291, A.293, Q.322 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:A.290, D:A.293, H2O.26, H2O.32, H2O.32

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.4: 15 residues within 4Å: Chain B: Y.103, S.105, G.106, W.107, D.122, D.167, H.194, X.205, R.242, W.297, N.327, F.359, T.361, L.362 Ligands: MG.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.297, B:T.361 Hydrogen bonds: B:S.105, B:G.106, B:W.107, B:R.242 Water bridges: B:K.203, B:K.203, B:K.203 PYR.7: 15 residues within 4Å: Chain C: Y.103, S.105, G.106, W.107, D.122, D.167, H.194, X.205, R.242, W.297, N.327, F.359, T.361, L.362 Ligands: MG.8 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.297, C:T.361 Hydrogen bonds: C:S.105, C:G.106, C:W.107, C:R.242 Water bridges: C:K.203, C:K.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ray, S. et al., The Nitro Group as a Masked Electrophile in Covalent Enzyme Inhibition. ACS Chem. Biol. (2018)

Release Date

2018-06-06

Peptides

Isocitrate lyase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isocitrate lyase 1

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