SMTL ID : 6c4c.2 (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

3 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 16 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, E.299, N.327, F.359, T.361, L.362 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.297, A:T.361 Hydrogen bonds: A:S.105, A:G.106, A:W.107, A:D.167, A:R.242 Water bridges: A:K.203, A:K.203, A:K.203, A:K.203 PYR.5: 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.6 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, B:T.361 Water bridges: B:K.203, B:K.203 PYR.7: 17 residues within 4Å: Chain C: Y.103, S.105, G.106, W.107, D.122, D.167, H.194, K.203, X.205, R.242, W.297, E.299, N.327, F.359, T.361, L.362 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.297, C:T.361 Hydrogen bonds: C:S.105, C:G.106, C:W.107, C:D.122, C:R.242 Water bridges: C:K.203, C:K.203, C: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: PYR.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: 4 residues within 4Å: Chain A: D.39, 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.1, H2O.7, H2O.8 MG.6: 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.5 5 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:D.167, PYR.5, H2O.9, H2O.10, H2O.11 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 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.167, H2O.15, H2O.16, H2O.17 MG.9: 5 residues within 4Å: Chain C: A.290, P.291, A.293, D.294, Q.322 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.290, C:A.293, H2O.20, H2O.22 MG.10: 1 residues within 4Å: Chain D: D.48 No protein-ligand interaction detected (PLIP) MG.12: 9 residues within 4Å: Chain D: G.106, W.107, D.122, D.167, E.169, H.194, K.203, X.205 Ligands: GLV.11 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.167, H2O.23, H2O.23, H2O.24 MG.13: 3 residues within 4Å: Chain D: A.290, 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.29, H2O.29

1 x 3NP: 3-NITROPROPANOIC ACID(Non-covalent)

3NP.4: 8 residues within 4Å: Chain A: Y.370, S.371, L.390, R.393 Chain B: Y.370, S.371, L.390, R.393 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:R.393, A:D.374 Salt bridges: B:R.393 Hydrophobic interactions: A:Y.370

1 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.11: 14 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, F.359, T.361, L.362 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Y.103, D:S.105, D:G.106, D:W.107, D:D.167, D:R.242 Water bridges: D:K.203, D: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
E

B
F

C
G

D
H

Isocitrate lyase 1

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