SMTL ID : 4g09.1

The crystal structure of the C366S mutant of HDH from Brucella suis in complex with a substituted benzyl ketone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.262, D.361 Chain B: H.420 Ligands: DMS.4, 0VD.5 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:H.420, A:H.262, A:D.361, DMS.4 ZN.2: 2 residues within 4Å: Chain A: D.313, D.316 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.313, A:D.313, A:D.316, A:D.316 ZN.6: 5 residues within 4Å: Chain A: H.420 Chain B: H.262, D.361 Ligands: DMS.9, 0VD.10 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:H.262, B:D.361, A:H.420, DMS.9 ZN.7: 2 residues within 4Å: Chain B: D.313, D.316 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.313, B:D.313, B:D.316, B:D.316

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: F.56, G.189, Q.191, N.214, Y.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.191, A:Q.191, A:N.214 Water bridges: A:A.190 GOL.8: 5 residues within 4Å: Chain B: F.56, G.189, Q.191, N.214, Y.216 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.191, B:Q.191, B:N.214 Water bridges: B:A.190

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 10 residues within 4Å: Chain A: A.258, Q.259, H.262, H.328, E.357, V.358, D.361 Chain B: H.420 Ligands: ZN.1, 0VD.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.259, A:E.357 Salt bridges: A:E.357, A:D.361 DMS.9: 10 residues within 4Å: Chain A: H.420 Chain B: A.258, Q.259, H.262, H.328, E.357, V.358, D.361 Ligands: ZN.6, 0VD.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.259 Salt bridges: B:E.357, B:D.361

2 x 0VD: (3S)-3-amino-1-[4-(benzyloxy)phenyl]-4-(1H-imidazol-4-yl)butan-2-one(Non-covalent)

0VD.5: 17 residues within 4Å: Chain A: P.132, A.136, Y.138, S.140, S.237, H.262, E.327, H.328, E.357, D.361, Y.362, H.368 Chain B: E.415, L.417, H.420 Ligands: ZN.1, DMS.4 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.132, A:A.136, A:D.361 Hydrogen bonds: A:S.140, A:D.361, A:Y.362, B:E.415 Water bridges: A:S.141 pi-Stacking: A:H.262 pi-Cation interactions: A:H.262 0VD.10: 17 residues within 4Å: Chain A: E.415, L.417, H.420 Chain B: P.132, A.136, Y.138, S.140, S.237, H.262, E.327, H.328, E.357, D.361, Y.362, H.368 Ligands: ZN.6, DMS.9 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.132, B:A.136, B:D.361 Hydrogen bonds: B:S.140, B:D.361, A:E.415 Water bridges: B:S.141 pi-Stacking: B:H.262 pi-Cation interactions: B:H.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

D'ambrosio, K. et al., Structural basis for the rational design of new anti-Brucella agents: The crystal structure of the C366S mutant of l-histidinol dehydrogenase from Brucella suis. Biochimie (2014)

Release Date

2013-10-02

Peptides

Histidinol dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histidinol dehydrogenase

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