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

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x L4M: 4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}benzoic acid(Non-covalent)

L4M.1: 19 residues within 4Å: Chain A: T.18, G.19, K.22, T.48, R.52, D.54, P.78, M.79, A.80, P.81, A.117, G.118, V.122 Chain B: L.150, G.151, T.152, L.153, N.154 Ligands: SO4.2 17 PLIP interactions: 5 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:L.150, A:P.78, A:A.80, A:V.122, A:V.122 Hydrogen bonds: B:G.151, B:L.153, B:N.154, A:T.18, A:T.18, A:G.19, A:G.118 Water bridges: B:N.154, A:K.44, A:E.115 Salt bridges: A:K.22, A:K.44 L4M.3: 18 residues within 4Å: Chain A: L.150, G.151, T.152, L.153, N.154 Chain B: T.18, G.19, K.22, T.48, R.52, D.54, P.78, M.79, A.80, A.117, G.118, V.122 Ligands: SO4.4 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.80, B:V.122, A:L.150 Hydrogen bonds: B:G.19, B:G.118, A:G.151, A:L.153, A:N.154 Water bridges: B:T.23, B:K.44, B:K.44, B:D.56, B:D.56, A:N.154 Salt bridges: B:K.22

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: G.19, V.20, G.21, K.22, T.23 Ligands: L4M.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.19, A:V.20, A:G.21, A:K.22, A:T.23 Water bridges: A:T.23, A:T.23, A:E.115 Salt bridges: A:K.22 SO4.4: 6 residues within 4Å: Chain B: G.19, V.20, G.21, K.22, T.23 Ligands: L4M.3 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.19, B:V.20, B:G.21, B:K.22, B:T.23, B:T.23 Water bridges: B:T.23, B:T.23, B:V.24, B:D.56, B:E.115 Salt bridges: B:K.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, A.P. et al., Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 7. To Be Published

Release Date

2020-02-12

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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