SMTL ID : 5dql.1

Crystal Structure of 2-vinyl glyoxylate modified isocitrate lyase from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-tetramer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.108, D.153 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.153, H2O.1, H2O.2, H2O.8, H2O.11 MG.2: 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.3, H2O.3, H2O.11 MG.4: 5 residues within 4Å: Chain B: G.92, W.93, D.108, D.153 Ligands: VGX.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.153, H2O.15, H2O.17, H2O.17, H2O.23 MG.6: 3 residues within 4Å: Chain C: W.93, D.108, D.153 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.153, H2O.27, H2O.30, H2O.32, H2O.34 MG.8: 4 residues within 4Å: Chain D: G.92, W.93, D.108, D.153 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.153, H2O.37, H2O.40, H2O.42, H2O.46

4 x VGX: 4-hydroxy-2-oxobutanoic acid(Covalent)

VGX.3: 10 residues within 4Å: Chain A: W.93, D.108, C.191, G.192, H.193, N.313, S.315, S.317, T.347, L.348 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.93 Hydrogen bonds: A:N.313, A:S.315, A:S.317, A:T.347, A:T.347 Salt bridges: A:H.193 VGX.5: 11 residues within 4Å: Chain B: W.93, D.108, C.191, G.192, H.193, N.313, S.315, S.317, T.347, L.348 Ligands: MG.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.93 Hydrogen bonds: B:N.313, B:S.315, B:S.317 Water bridges: B:G.192 Salt bridges: B:H.193 VGX.7: 10 residues within 4Å: Chain C: W.93, D.108, C.191, G.192, H.193, N.313, S.315, S.317, T.347, L.348 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.313, C:S.315, C:S.317, C:T.347, C:T.347 Water bridges: C:W.93 Salt bridges: C:H.193 VGX.9: 11 residues within 4Å: Chain C: Q.394 Chain D: W.93, D.108, C.191, G.192, H.193, N.313, S.315, S.317, T.347, L.348 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.313, D:S.315, D:S.317 Salt bridges: D:H.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pham, T.V. et al., Mechanism-based inactivator of isocitrate lyases 1 and 2 from Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2016-09-14

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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