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

Crystal structure of Mycobacterium tuberculosis dethiobiotin Synthetase in complex with cytidine triphosphate and 7,8-diaminopelargonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

CTP.1: 19 residues within 4Å: Chain A: T.20, G.21, V.22, G.23, K.24, T.25, V.26, D.58, E.117, G.120, G.178, S.179, L.205, P.206, G.208, A.209, A.210 Ligands: MG.2, DSD.3 19 PLIP interactions: 19 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.120, A:G.178, A:G.208, A:A.209, A:A.210 Water bridges: A:D.58, A:D.58, A:D.58 Salt bridges: A:K.24, A:K.24, A:K.46

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.25, D.58, E.117 Ligands: CTP.1 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

1 x DSD: 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID(Non-covalent)

DSD.3: 16 residues within 4Å: Chain A: T.20, K.46, Q.49, T.50, P.80, M.81, A.82, A.119, G.120, V.124 Chain B: L.152, G.153, T.154, L.155, N.156 Ligands: CTP.1 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:G.153, B:L.155, B:N.156, A:T.20, A:K.46, A:T.50, A:T.50, A:G.120 Water bridges: B:N.156, B:N.156, A:Q.49, A:Q.49 Hydrophobic interactions: A:A.82, A:V.124

1 x FLC: CITRATE ANION(Non-covalent)

FLC.4: 9 residues within 4Å: Chain B: G.21, V.22, G.23, K.24, T.25, V.26, D.58, E.117, G.120 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.21, B:V.22, B:G.23, B:K.24, B:T.25, B:V.26, B:G.120 Water bridges: B:T.25, B:K.46 Salt bridges: B:K.24, B:K.24, B:K.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, A.P. et al., Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes. Acs Catalysis (2018)

Release Date

2018-11-21

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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