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

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with an intentionally produced fragment degradation product B9D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: G.19, V.20, G.21, K.22, T.23 Ligands: KSJ.3, KSP.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.19, A:V.20, A:G.21, A:K.22, A:T.23, A:T.23 Salt bridges: A:K.22 SO4.2: 7 residues within 4Å: Chain A: G.151, T.152, L.153, N.154 Chain B: V.122 Ligands: KSJ.7, KSP.8 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.151, A:L.153, A:N.154 Water bridges: A:T.152, A:N.154, B:T.18 SO4.5: 8 residues within 4Å: Chain B: T.18, G.19, V.20, G.21, K.22, T.23 Ligands: KSJ.7, KSP.8 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 SO4.6: 9 residues within 4Å: Chain A: A.80, V.122 Chain B: L.150, G.151, T.152, L.153, N.154 Ligands: KSJ.3, KSP.4 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:T.18, B:T.152 Hydrogen bonds: B:G.151, B:L.153, B:N.154

2 x KSJ: [(1S,2R)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid(Non-covalent)

KSJ.3: 17 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 Ligands: SO4.1, KSP.4, SO4.6 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.78, A:A.80, A:V.122, A:V.122, B:L.150, B:L.150 Hydrogen bonds: A:G.19, A:G.118 Water bridges: A:K.44 Salt bridges: A:K.22, A:K.44 KSJ.7: 18 residues within 4Å: Chain A: L.150, G.151 Chain B: T.18, G.19, K.22, K.44, T.48, R.52, D.54, M.79, A.80, P.81, A.117, G.118, V.122 Ligands: SO4.2, SO4.5, KSP.8 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.80, B:V.122, A:L.150, A:L.150 Hydrogen bonds: B:T.18, B:G.19, B:G.118 Water bridges: B:K.22, B:K.22 Salt bridges: B:K.22, B:K.44

2 x KSP: [(1R,2S)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid(Non-covalent)

KSP.4: 16 residues within 4Å: Chain A: T.18, G.19, K.22, T.48, R.52, P.78, M.79, A.80, P.81, A.117, G.118, V.122 Chain B: L.150 Ligands: SO4.1, KSJ.3, SO4.6 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.18, A:T.18, A:P.78, A:A.80, A:V.122, A:V.122, B:L.150, B:L.150 Hydrogen bonds: A:G.19, A:G.118 Water bridges: A:K.44 Salt bridges: A:K.22, A:K.44 KSP.8: 18 residues within 4Å: Chain A: L.150, G.151 Chain B: T.18, G.19, K.22, K.44, T.48, R.52, P.78, M.79, A.80, P.81, A.117, G.118, V.122 Ligands: SO4.2, SO4.5, KSJ.7 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.80, B:V.122, A:L.150, A:L.150 Hydrogen bonds: B:T.18, B:G.19, B:G.118 Water bridges: B:K.22, B:K.22 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 an intentionally produced fragment degradation product B9D. To Be Published

Release Date

2020-01-22

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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