SMTL ID : 6e05.1 (1 other biounit)

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine triphosphate solved by precipitant-ligand exchange (crystals grown in sulfate precipitant)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.25, D.58, E.117 Ligands: CTP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.25, A:D.58, A:E.117, H2O.2 MG.3: 5 residues within 4Å: Chain B: T.25, K.46, D.58, E.117 Ligands: CTP.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.25, B:D.58, B:E.117, H2O.6

2 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.2: 17 residues within 4Å: Chain A: T.20, G.21, V.22, G.23, K.24, T.25, V.26, D.58, E.117, G.178, S.179, L.205, P.206, G.208, A.209, A.210 Ligands: MG.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.20, A:G.21, A:V.22, A:G.23, A:K.24, A:T.25, A:V.26, A:E.117, A:G.178, A:G.208, A:A.209, A:A.210 Water bridges: A:D.58, A:S.179 Salt bridges: A:K.24, A:K.24 CTP.4: 18 residues within 4Å: Chain B: T.20, G.21, V.22, G.23, K.24, T.25, V.26, E.117, G.120, G.178, S.179, L.205, P.206, A.207, G.208, A.209, A.210 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.26 Hydrogen bonds: B:G.21, B:V.22, B:G.23, B:K.24, B:T.25, B:T.25, B:V.26, B:G.120, B:P.206, B:G.208, B:A.209, B:A.210 Water bridges: B:S.179 Salt bridges: B:K.24, B:K.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, A.P. et al., Precipitant-ligand exchange technique reveals the ADP binding mode in Mycobacterium tuberculosis dethiobiotin synthetase. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-10-17

Peptides

ATP-dependent dethiobiotin synthetase BioD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent dethiobiotin synthetase BioD

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