SMTL ID : 6c4a.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 15 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, 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:R.242 Water bridges: A:G.106, A:D.122, A:K.203, A:K.203, A:K.203 PYR.6: 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.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.297, B:T.361 Hydrogen bonds: B:S.105, B:G.106, B:W.107, B:D.167, B:R.242 Water bridges: B:K.203, B:K.203, B:K.203, B:K.203, B:K.203 PYR.11: 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.12 11 PLIP interactions: 11 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:G.106, C:D.122, C:K.203, C:K.203, C:K.203 PYR.18: 15 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, N.327, F.359, T.361, L.362 Ligands: MG.19 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.297, D:T.361 Hydrogen bonds: D:S.105, D:G.106, D:W.107, D:R.242 Water bridges: D:K.203, D:K.203, D:K.203

12 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

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.2, H2O.3 MG.3: 4 residues within 4Å: Chain A: A.290, P.291, 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.13, H2O.13 MG.7: 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.6 5 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:D.167, PYR.6, H2O.17, H2O.17, H2O.18 MG.8: 1 residues within 4Å: Chain B: D.374 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: D.39, A.290, 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.20, H2O.28, H2O.28 MG.12: 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.11 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.167, H2O.31, H2O.32, H2O.34 MG.14: 4 residues within 4Å: Chain C: D.39, A.290, 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.31, H2O.42, H2O.42 MG.16: 1 residues within 4Å: Chain D: N.333 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain D: D.48 No protein-ligand interaction detected (PLIP) MG.19: 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: PYR.18 5 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: D:D.167, PYR.18, H2O.46, H2O.47, H2O.47 MG.20: 1 residues within 4Å: Chain D: R.393 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain D: A.290, A.293, D.294, Q.322 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:A.290, D:A.293, H2O.47, H2O.56, H2O.57

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: E.78, W.79, V.80, N.81 Chain B: A.380, Q.381, Q.383 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.381, B:Q.383, B:Q.383, A:N.81, A:N.81 PEG.10: 7 residues within 4Å: Chain A: Q.383 Chain B: L.77, E.78, W.79, V.80, N.81, K.100 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:Q.383, B:N.81, B:N.81 Hydrogen bonds: B:N.81 PEG.15: 5 residues within 4Å: Chain C: E.78, W.79, N.81, K.348 Chain D: Q.383 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.348 PEG.22: 6 residues within 4Å: Chain C: A.380, Q.383 Chain D: E.78, W.79, V.80, N.81 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.79

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 8 residues within 4Å: Chain A: Y.370, S.371, R.393 Chain B: Y.370, S.371, D.374, L.390, R.393 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.374 Water bridges: B:R.393 Salt bridges: B:R.393 EPE.13: 8 residues within 4Å: Chain C: Y.370, S.371, D.374, L.390, R.393 Chain D: Y.370, S.371, R.393 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Water bridges: C:R.393, D:R.393 Salt bridges: C:D.374, C:R.393

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

Related Entries With Identical Sequence