SMTL ID : 7ut5.1 (1 other biounit)

Acinetobacter baumannii dihydroorotate dehydrogenase bound with inhibitor DSM186

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x OBR: (4R)-7-methyl-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl]imidazo[1,2-a]pyrimidin-5-amine(Non-covalent)

OBR.1: 19 residues within 4Å: Chain A: Y.23, R.27, L.30, F.31, P.35, A.38, H.39, T.42, L.43, L.46, L.81, L.91, L.94, L.117, R.119, I.126, L.338, I.339, P.343 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.23, A:L.30, A:F.31, A:A.38, A:T.42, A:T.42, A:L.43, A:L.81, A:I.339 Hydrogen bonds: A:H.39, A:R.119, A:R.119

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 30 residues within 4Å: Chain A: A.78, A.79, G.80, K.83, G.102, T.103, L.117, I.126, N.128, M.130, F.132, N.156, N.189, K.234, T.262, N.263, T.264, S.284, G.285, V.288, V.312, G.313, G.314, I.315, I.334, Y.335, S.336, G.337, I.339 Ligands: ORO.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.117, A:N.128 Hydrogen bonds: A:K.83, A:T.103, A:T.103, A:N.156, A:N.189, A:K.234, A:T.262, A:N.263, A:N.263, A:S.284, A:G.285, A:G.313, A:G.314, A:I.315, A:Y.335, A:S.336, A:S.336 pi-Stacking: A:Y.335

1 x ORO: OROTIC ACID(Non-covalent)

ORO.3: 12 residues within 4Å: Chain A: K.83, N.128, R.129, M.130, G.131, F.132, N.189, N.263, T.264, G.282 Ligands: FMN.2, GOL.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.132 Hydrogen bonds: A:N.128, A:N.128, A:N.128, A:M.130, A:G.131, A:F.132, A:N.189, A:N.263, A:N.263, A:T.264 Salt bridges: A:K.83

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: N.128, R.129, M.130, G.131, T.264, L.266, G.281, G.282 Ligands: ORO.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.128, A:T.264, A:G.281 Water bridges: A:N.263, A:T.264 GOL.5: 5 residues within 4Å: Chain A: A.34, P.35, P.115, F.118, Y.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.276 GOL.6: 5 residues within 4Å: Chain A: T.103, F.132, G.158, K.159, Y.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.159, A:K.159, A:Y.172 Water bridges: A:Y.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Russo, T.A. et al., Repurposed dihydroorotate dehydrogenase inhibitors with efficacy against drug-resistant Acinetobacter baumannii. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-12-28

Peptides

Dihydroorotate dehydrogenase (quinone): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone)

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