SMTL ID : 6ovt.1

Crystal Structure of IlvD from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 6 residues within 4Å: Chain A: D.121, D.163, K.164, T.244, N.317, E.490 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.121, A:D.163, A:E.490, H2O.1, H2O.2 MG.3: 1 residues within 4Å: Chain A: D.94 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.94, H2O.3, H2O.9, H2O.10, H2O.11, H2O.13 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain B: D.121, D.163, K.164, T.244, E.490 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.121, B:D.163, B:E.490, H2O.19, H2O.23 MG.9: 1 residues within 4Å: Chain B: D.94 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.94, H2O.17, H2O.20, H2O.23, H2O.24 MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain C: D.121, D.163, K.164, T.244, E.490 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.121, C:D.163, C:E.490, H2O.30, H2O.34 MG.14: 1 residues within 4Å: Chain C: D.94 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.94, H2O.31, H2O.31, H2O.32, H2O.32, H2O.35 MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain D: D.121, D.163, K.164, T.244, E.490 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.121, D:D.163, H2O.45, H2O.45 MG.17: 1 residues within 4Å: Chain D: D.94 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.94, H2O.39, H2O.43, H2O.44, H2O.45, H2O.47 MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 9 residues within 4Å: Chain A: C.89, S.120, D.121, G.122, C.162, D.163, A.238, C.239 Chain C: M.61 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.89, A:C.162, A:C.239, H2O.7 FES.7: 8 residues within 4Å: Chain B: C.89, G.122, C.162, D.163, A.238, C.239, A.245 Chain D: M.61 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.89, B:C.162, B:C.239, H2O.21 FES.11: 9 residues within 4Å: Chain A: M.61 Chain C: C.89, D.121, G.122, C.162, D.163, A.238, C.239, A.245 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.89, C:C.162, C:C.239, H2O.30 FES.18: 9 residues within 4Å: Chain B: M.61 Chain D: C.89, D.121, G.122, C.162, D.163, A.238, C.239, A.245 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.89, D:C.162, D:C.239, H2O.45

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

PEG.5: 6 residues within 4Å: Chain A: I.341, V.345, G.379, L.380, L.381, H.382 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.341 PEG.8: 5 residues within 4Å: Chain B: I.341, G.379, L.380, L.381, H.382 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.382 PEG.12: 7 residues within 4Å: Chain C: I.341, G.344, V.345, G.379, L.380, L.381, H.382 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.382

1 x NA: SODIUM ION(Non-functional Binders)

NA.20: 4 residues within 4Å: Chain D: D.455, G.456, R.458, A.459 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.455, D:R.458, D:A.459 Water bridges: D:E.457

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bashiri, G. et al., The active site of theMycobacterium tuberculosisbranched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster. J.Biol.Chem. (2019)

Release Date

2019-08-07

Peptides

Dihydroxy-acid dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dihydroxy-acid dehydratase