SMTL ID : 5drr.1

Crystal structure of the Pseudomonas aeruginosa LpxC/LPC-058 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.78, H.237, D.241 Ligands: 5EN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.78, A:H.237, A:D.241, A:D.241 ZN.2: 2 residues within 4Å: Chain A: H.162, E.219 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.162, A:E.219, A:E.219

1 x 5EN: 4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3S)-4,4-difluoro-3-hydroxy-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]benzamide(Non-covalent)

5EN.3: 17 residues within 4Å: Chain A: L.18, M.62, E.77, H.78, T.190, F.191, I.197, R.201, G.209, S.210, V.211, V.216, H.237, K.238, D.241, H.264 Ligands: ZN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.18, A:T.190, A:I.197, A:I.197, A:I.197, A:V.211, A:V.216 Hydrogen bonds: A:M.62, A:T.190, A:T.190 Halogen bonds: A:K.238

17 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 8 residues within 4Å: Chain A: I.158, R.168, T.169, Q.170, D.232, E.233, F.234, V.235 Ligand excluded by PLIP NO3.5: 4 residues within 4Å: Chain A: R.168, V.222, G.227, L.228 Ligand excluded by PLIP NO3.6: 4 residues within 4Å: Chain A: E.184, Y.230, K.236 Ligands: NO3.20 Ligand excluded by PLIP NO3.7: 4 residues within 4Å: Chain A: I.2, A.289, S.295, Y.296 Ligand excluded by PLIP NO3.8: 5 residues within 4Å: Chain A: H.19, M.62, L.200, L.205, A.206 Ligand excluded by PLIP NO3.9: 4 residues within 4Å: Chain A: S.136, V.137, E.138, R.143 Ligand excluded by PLIP NO3.10: 3 residues within 4Å: Chain A: V.137, E.138, Q.269 Ligand excluded by PLIP NO3.11: 6 residues within 4Å: Chain A: F.152, F.176, S.177, P.293, I.294, S.295 Ligand excluded by PLIP NO3.12: 4 residues within 4Å: Chain A: T.14, G.15, V.16, K.23 Ligand excluded by PLIP NO3.13: 6 residues within 4Å: Chain A: K.142, S.262, G.263, H.264, A.265, L.266 Ligand excluded by PLIP NO3.14: 3 residues within 4Å: Chain A: R.189, D.226, R.229 Ligand excluded by PLIP NO3.15: 5 residues within 4Å: Chain A: E.134, R.143, V.145, R.258, F.260 Ligand excluded by PLIP NO3.16: 4 residues within 4Å: Chain A: I.158, D.159, F.160, K.261 Ligand excluded by PLIP NO3.17: 3 residues within 4Å: Chain A: R.133, E.134, P.148 Ligand excluded by PLIP NO3.18: 3 residues within 4Å: Chain A: P.148, F.149, D.150 Ligand excluded by PLIP NO3.19: 3 residues within 4Å: Chain A: Q.269, R.272, T.273 Ligand excluded by PLIP NO3.20: 5 residues within 4Å: Chain A: Y.230, E.231, D.232, K.236 Ligands: NO3.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C.J. et al., Drug design from the cryptic inhibitor envelope. Nat Commun (2016)

Release Date

2016-03-09

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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