SMTL ID : 6nvc.2 (1 other biounit)

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: T.18, G.19, V.20, G.21, K.22, T.23, E.115 Ligands: L67.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.19, A:V.20, A:G.21, A:K.22, A:T.23, A:T.23, A:E.115 Salt bridges: A:K.22 SO4.4: 7 residues within 4Å: Chain B: G.19, V.20, G.21, K.22, T.23, E.115 Ligands: L67.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.19, B:V.20, B:G.21, B:K.22, B:T.23 Salt bridges: B:K.22

2 x L67: {(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetic acid(Non-covalent)

L67.2: 20 residues within 4Å: Chain A: T.18, K.22, K.44, T.48, R.52, D.54, D.56, 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: SO4.1 22 PLIP interactions: 15 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:T.18, A:P.78, A:A.80, A:V.122, A:V.122, B:L.150, B:L.150 Hydrogen bonds: A:D.56, A:G.118, B:G.151, B:L.153, B:N.154 Water bridges: A:K.44, A:K.44, A:K.44, A:K.44, A:Q.47, A:G.119, B:G.151, B:N.154 Salt bridges: A:K.22, A:K.44 L67.3: 19 residues within 4Å: Chain A: L.150, G.151, T.152, L.153, N.154 Chain B: T.18, K.22, K.44, T.48, R.52, D.54, P.78, M.79, A.80, P.81, A.117, G.118, V.122 Ligands: SO4.4 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:L.150, B:P.78, B:A.80, B:A.117, B:V.122, B:V.122 Hydrogen bonds: A:G.151, A:L.153, A:N.154, B:T.18, B:T.18, B:G.118 Water bridges: B:K.44 Salt bridges: B:K.22, B:K.44

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 6. To Be Published

Release Date

2020-02-12

Peptides

ATP-dependent dethiobiotin synthetase BioD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

ATP-dependent dethiobiotin synthetase BioD

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