SMTL ID : 6c4a.1 (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 12 PLIP interactions: 12 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:D.167, A:R.242 Water bridges: A:K.203, 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 10 PLIP interactions: 10 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, B:K.203 PYR.10: 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.11 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 PYR.15: 16 residues within 4Å: Chain D: Y.103, S.105, G.106, W.107, D.122, D.167, H.194, K.203, X.205, R.242, W.297, N.327, F.359, T.361, L.362 Ligands: MG.16 10 PLIP interactions: 10 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, D:K.203

9 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.1, H2O.2 MG.3: 5 residues within 4Å: Chain A: D.39, 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.2, H2O.10, H2O.10 MG.4: 1 residues within 4Å: Chain A: R.400 No protein-ligand interaction detected (PLIP) MG.7: 9 residues within 4Å: Chain B: G.106, W.107, D.122, D.167, E.169, H.194, K.203, R.242 Ligands: PYR.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.167, H2O.13, H2O.13, H2O.15 MG.8: 3 residues within 4Å: Chain B: 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.17, H2O.20, H2O.21 MG.11: 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.10 5 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: C:D.167, PYR.10, H2O.23, H2O.24, H2O.24 MG.12: 3 residues within 4Å: Chain C: 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.28, H2O.31, H2O.33 MG.16: 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.15 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.167, H2O.35, H2O.36, H2O.37 MG.17: 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.42, H2O.44, H2O.45

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

3NP.5: 9 residues within 4Å: Chain A: Y.370, S.371, L.390, R.393 Chain B: A.367, Y.370, S.371, L.390, R.393 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.370 Water bridges: B:D.374, A:R.393 Salt bridges: A:R.393 3NP.14: 11 residues within 4Å: Chain C: A.367, Y.370, S.371, D.374, L.390, R.393 Chain D: A.367, Y.370, S.371, L.390, R.393 3 PLIP interactions: 3 interactions with chain C Water bridges: C:D.374, C:R.393 Salt bridges: C:R.393

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

PEG.9: 5 residues within 4Å: Chain A: A.380, Q.383 Chain B: L.77, E.78, W.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.78 PEG.13: 4 residues within 4Å: Chain C: E.78, W.79, N.81 Chain D: Q.383 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:E.78, C:N.81, D:Q.383 PEG.18: 7 residues within 4Å: Chain C: A.380, Q.381, Q.383 Chain D: E.78, W.79, V.80, N.81 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.383, D:W.79 Water bridges: D:N.81

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

Related Entries With Identical Sequence