SMTL ID : 8uw6.1 (1 other biounit)

Acetylornithine deacetylase from Escherichia coli, di-zinc form.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.83, D.115, E.147, E.148, E.172 Ligands: ZN.2, TRS.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.83, A:D.115, A:E.172, A:E.172 ZN.2: 5 residues within 4Å: Chain A: D.115, E.148, H.358 Ligands: ZN.1, TRS.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.115, A:E.148, A:E.148, A:H.358 ZN.3: 4 residues within 4Å: Chain A: H.381, H.386 Chain B: H.381, H.386 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.381, A:H.386, B:H.381, B:H.386 ZN.6: 7 residues within 4Å: Chain B: H.83, D.115, E.147, E.148, E.172 Ligands: ZN.7, TRS.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.83, B:D.115, B:E.172, B:E.172 ZN.7: 5 residues within 4Å: Chain B: D.115, E.148, H.358 Ligands: ZN.6, TRS.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.115, B:E.148, B:E.148, B:H.358

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 12 residues within 4Å: Chain A: H.83, D.115, E.147, E.148, E.172, P.173, Y.333, C.334, I.354, H.358 Ligands: ZN.1, ZN.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.358 TRS.5: 8 residues within 4Å: Chain A: E.147, E.148, T.149, M.151, H.185, H.302, I.305, C.334 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.147, A:H.185 Water bridges: A:E.148 TRS.10: 12 residues within 4Å: Chain B: H.83, D.115, E.147, E.148, E.172, P.173, Y.333, C.334, I.354, H.358 Ligands: ZN.6, ZN.7 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.173, B:H.358

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

SO4.8: 2 residues within 4Å: Chain B: H.198, N.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.254 Salt bridges: B:H.198 SO4.9: 4 residues within 4Å: Chain B: N.52, T.71, G.72, Q.73 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.52, B:G.72, B:Q.73 Water bridges: B:G.72, B:Q.73 SO4.12: 3 residues within 4Å: Chain B: H.185, R.267 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.185, B:R.267

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 5 residues within 4Å: Chain B: H.185, H.302, I.305, C.334 Ligands: SO4.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kelley, E.H. et al., N alpha-acetyl-L-ornithine deacetylase from Escherichia coli and a ninhydrin-based assay to enable inhibitor identification. Front Chem (2024)

Release Date

2024-05-29

Peptides

Acetylornithine deacetylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Acetylornithine deacetylase

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