SMTL ID : 2ier.1

Crystal Structure of Aquifex aeolicus LpxC Complexed with Uridine 5'-Diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.74, T.179, H.226, D.230 Ligands: ZN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.74, A:H.226, A:D.230, A:D.230, H2O.1 ZN.2: 2 residues within 4Å: Chain A: H.58, H.188 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.58, A:H.188 ZN.3: 5 residues within 4Å: Chain A: G.2, E.120 Chain B: I.27, H.29, E.90 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.29, B:E.90, B:E.90, A:E.120, A:E.120 ZN.4: 6 residues within 4Å: Chain A: H.58, S.59, E.73, D.230, H.253 Ligands: ZN.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.73, A:H.253, H2O.1, H2O.2 ZN.5: 3 residues within 4Å: Chain A: H.58 Ligands: UDP.6, PLM.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.58 ZN.9: 5 residues within 4Å: Chain B: H.74, T.179, H.226, D.230 Ligands: ZN.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.74, B:H.226, B:D.230, B:D.230, H2O.2 ZN.10: 2 residues within 4Å: Chain B: H.58, H.188 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.58, B:H.188 ZN.11: 5 residues within 4Å: Chain B: H.58, S.59, E.73, H.253 Ligands: ZN.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.73, B:H.253, H2O.2 ZN.12: 3 residues within 4Å: Chain B: H.58 Ligands: UDP.13, PLM.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.58

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.6: 15 residues within 4Å: Chain A: T.56, H.58, Y.151, G.153, E.154, F.155, F.180, F.182, E.185, K.227, R.250, G.252, H.253 Ligands: ZN.5, PLM.7 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:H.58, A:E.154, A:E.154, A:H.253 Water bridges: A:R.137, A:R.137, A:K.227, A:K.227, A:K.227, A:S.254 Salt bridges: A:R.137, A:K.227, A:K.227, A:H.253 pi-Stacking: A:F.155 UDP.13: 15 residues within 4Å: Chain B: T.56, H.58, Y.151, G.153, E.154, F.155, F.180, F.182, E.185, K.227, R.250, G.252, H.253 Ligands: ZN.12, PLM.14 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.58, B:E.154, B:E.154, B:H.253 Water bridges: B:K.227 Salt bridges: B:K.227, B:K.227, B:H.253 pi-Stacking: B:F.155

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.7: 13 residues within 4Å: Chain A: I.18, H.19, H.58, F.180, A.181, E.185, I.186, I.189, G.195, G.198, S.199 Ligands: ZN.5, UDP.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.18, A:A.181, A:I.186, A:I.189 PLM.14: 10 residues within 4Å: Chain B: I.18, H.19, H.58, E.185, I.186, G.198, S.199, Y.212 Ligands: ZN.12, UDP.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.18, B:I.186

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: H.80, E.83, Y.123, L.147, E.168, P.241, V.242, K.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.80, A:K.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gennadios, H.A. et al., Binding of Uridine 5-Diphosphate in the Basic Patch of the Zinc Metalloenzyme Deacetylase LpxC and Implications for Substrate Binding. Biochemistry (2006)

Release Date

2007-01-09

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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