SMTL ID : 1yhc.2 (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

homo-dimer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.73, T.178, H.225, D.229 Ligands: CAC.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.73, A:H.225, A:D.229, A:D.229 ZN.2: 5 residues within 4Å: Chain A: G.1, E.119 Chain B: I.26, H.28, E.89 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.28, B:E.89, B:E.89, A:E.119, A:E.119 ZN.3: 4 residues within 4Å: Chain A: H.57, H.187 Ligands: CL.6, CL.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.57, A:H.187 ZN.10: 5 residues within 4Å: Chain B: H.73, T.178, H.225, D.229 Ligands: CAC.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.73, B:H.225, B:D.229, B:D.229 ZN.11: 3 residues within 4Å: Chain B: H.57, H.187 Ligands: CL.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.57, B:H.187

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.4: 11 residues within 4Å: Chain A: H.57, T.70, E.72, H.73, T.178, H.225, D.229, H.252 Ligands: ZN.1, SO4.5, PAM.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.72 CAC.12: 10 residues within 4Å: Chain B: H.57, E.72, H.73, T.178, H.225, D.229, H.252 Ligands: ZN.10, SO4.13, PAM.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.229 Water bridges: B:F.179

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

SO4.5: 7 residues within 4Å: Chain A: T.55, H.57, K.226, G.251, H.252 Ligands: CAC.4, PAM.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.57, A:H.252 Water bridges: A:T.55, A:K.226 Salt bridges: A:K.226, A:H.252 SO4.13: 7 residues within 4Å: Chain B: T.55, H.57, K.226, G.251, H.252 Ligands: CAC.12, PAM.15 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.57, B:H.252 Water bridges: B:T.55, B:K.226, B:K.226, B:K.226, B:S.253 Salt bridges: B:K.226, B:H.252

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

CL.6: 5 residues within 4Å: Chain A: N.56, H.57, H.187 Ligands: ZN.3, CL.7 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: H.57, H.187 Ligands: ZN.3, CL.6 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: H.57, H.187 Ligands: ZN.11 Ligand excluded by PLIP

2 x PAM: PALMITOLEIC ACID(Non-covalent)

PAM.8: 14 residues within 4Å: Chain A: I.17, H.18, H.57, F.179, I.185, I.188, K.189, G.194, G.197, S.198, L.199, V.204 Ligands: CAC.4, SO4.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.17, A:I.188, A:L.199, A:V.204 Hydrogen bonds: A:F.179 Salt bridges: A:H.57, A:K.226 PAM.15: 13 residues within 4Å: Chain B: I.17, H.18, H.57, T.178, E.184, I.185, I.188, G.194, G.197, S.198, V.204 Ligands: CAC.12, SO4.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.17, B:T.178, B:I.185, B:I.188, B:V.204, B:V.204 Hydrogen bonds: B:E.184 Salt bridges: B:H.57

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: V.52, H.54, T.55, K.260 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.55 Water bridges: A:T.55, A:T.55, A:K.260

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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