SMTL ID : 1yhc.4 (3 other biounits)

Crystal structure of Aquifex aeolicus LpxC deacetylase complexed with cacodylate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.73, T.178, H.225, D.229 Ligands: CAC.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.73, A:H.225, A:D.229, A:D.229 ZN.2: 3 residues within 4Å: Chain A: H.57, H.187 Ligands: CL.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.57, A:H.187

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.3: 10 residues within 4Å: Chain A: H.57, E.72, H.73, T.178, H.225, D.229, H.252 Ligands: ZN.1, SO4.4, PAM.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.179

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

SO4.4: 7 residues within 4Å: Chain A: T.55, H.57, K.226, G.251, H.252 Ligands: CAC.3, PAM.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.57, A:H.252 Water bridges: A:T.55, A:K.226, A:K.226, A:K.226, A:S.253 Salt bridges: A:K.226, A:H.252

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: H.57, H.187 Ligands: ZN.2 Ligand excluded by PLIP

1 x PAM: PALMITOLEIC ACID(Non-covalent)

PAM.6: 13 residues within 4Å: Chain A: I.17, H.18, H.57, T.178, E.184, I.185, I.188, G.194, G.197, S.198, V.204 Ligands: CAC.3, SO4.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.17, A:T.178, A:I.185, A:I.188, A:V.204, A:V.204 Salt bridges: A:H.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hernick, M. et al., UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine Deacetylase Functions through a General Acid-Base Catalyst Pair Mechanism. J.Biol.Chem. (2005)

Release Date

2005-02-15

Peptides

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

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