SMTL ID : 2go3.3 (2 other biounits)

Crystal structure of Aquifex aeolicus LpxC complexed with imidazole.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.74, T.179, H.226, D.230 Ligands: IMD.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.74, A:H.226, A:D.230, H2O.8, H2O.8 ZN.2: 4 residues within 4Å: Chain A: H.58, H.188 Ligands: CL.3, IMD.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.58, A:H.188 ZN.9: 5 residues within 4Å: Chain B: H.74, T.179, H.226, D.230 Ligands: IMD.15 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.74, B:H.226, B:D.230, H2O.16, H2O.16 ZN.10: 5 residues within 4Å: Chain A: I.27, H.29, E.90 Chain B: G.2, E.120 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.29, A:E.90, A:E.90, B:E.120, B:E.120 ZN.11: 4 residues within 4Å: Chain B: H.58, H.188 Ligands: CL.12, IMD.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.58, B:H.188

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

CL.3: 5 residues within 4Å: Chain A: N.57, H.58, H.188 Ligands: ZN.2, IMD.6 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: N.57, H.58, H.188 Ligands: ZN.11, IMD.14 Ligand excluded by PLIP

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.4: 10 residues within 4Å: Chain A: I.18, H.19, H.58, F.180, I.186, G.195, G.198, V.205, Y.212 Ligands: IMD.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.18, A:I.186, A:V.205

2 x MYR: MYRISTIC ACID(Non-covalent)

MYR.5: 5 residues within 4Å: Chain A: K.190, G.198, S.199, L.200, K.201 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.195, A:K.196 Salt bridges: A:K.190 MYR.13: 9 residues within 4Å: Chain B: I.18, H.58, F.180, E.185, I.189, G.195, G.198, S.199, V.205 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.18, B:V.205 Water bridges: B:H.58, B:H.58, B:K.227, B:K.227, B:K.227, B:K.227 Salt bridges: B:H.58

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.6: 4 residues within 4Å: Chain A: H.58, H.188 Ligands: ZN.2, CL.3 No protein-ligand interaction detected (PLIP) IMD.7: 9 residues within 4Å: Chain A: H.58, E.73, H.74, T.179, H.226, D.230, H.253 Ligands: ZN.1, PLM.4 No protein-ligand interaction detected (PLIP) IMD.14: 4 residues within 4Å: Chain B: H.58, H.188 Ligands: ZN.11, CL.12 No protein-ligand interaction detected (PLIP) IMD.15: 8 residues within 4Å: Chain B: H.58, E.73, H.74, T.179, H.226, D.230, H.253 Ligands: ZN.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.73

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: H.80, L.81, E.83, Y.123, L.147, E.168, P.241, V.242, K.243 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.80, A:E.83, A:K.243, A:K.243 Water bridges: A:Y.123 GOL.16: 9 residues within 4Å: Chain B: H.80, L.81, E.83, Y.123, L.147, E.168, P.241, V.242, K.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.81, B:K.243, B:K.243 GOL.17: 5 residues within 4Å: Chain B: V.53, V.54, H.55, T.56, K.261 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.56 Water bridges: B:T.56, B:T.56 GOL.18: 5 residues within 4Å: Chain A: K.10, H.29 Chain B: Y.123, D.145, K.243 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.10, B:D.145 Water bridges: A:H.29, B:G.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gennadios, H.A. et al., Mechanistic Inferences from the Binding of Ligands to LpxC, a Metal-Dependent Deacetylase. Biochemistry (2006)

Release Date

2006-07-04

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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