SMTL ID : 3p3e.1

Crystal Structure of the PSEUDOMONAS AERUGINOSA LpxC/LPC-009 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: E.77, H.78, T.190, H.237, D.241, H.264 Ligands: 3P3.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.78, A:H.237, A:D.241, A:D.241 ZN.2: 3 residues within 4Å: Chain A: H.162, P.163, E.219 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.162, A:E.219, A:E.219

1 x 3P3: N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide(Non-covalent)

3P3.3: 23 residues within 4Å: Chain A: L.18, M.62, S.63, E.77, H.78, T.190, F.191, G.192, I.197, L.200, R.201, A.206, G.209, S.210, V.211, A.214, V.216, H.237, K.238, D.241, H.264 Ligands: ZN.1, NO3.13 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.18, A:I.197, A:I.197, A:V.211, A:A.214 Hydrogen bonds: A:M.62, A:T.190, A:T.190, A:H.264 Water bridges: A:K.238

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NO3.5: 5 residues within 4Å: Chain A: E.134, R.143, V.145, R.258, F.260 Ligand excluded by PLIP NO3.6: 9 residues within 4Å: Chain A: I.158, F.165, R.168, T.169, Q.170, D.232, E.233, F.234, V.235 Ligand excluded by PLIP NO3.7: 3 residues within 4Å: Chain A: R.189, D.226, R.229 Ligand excluded by PLIP NO3.8: 3 residues within 4Å: Chain A: P.148, F.149, D.150 Ligand excluded by PLIP NO3.9: 5 residues within 4Å: Chain A: F.176, S.177, S.178, T.179, S.180 Ligand excluded by PLIP NO3.10: 4 residues within 4Å: Chain A: I.158, D.159, F.160, K.261 Ligand excluded by PLIP NO3.11: 3 residues within 4Å: Chain A: R.12, T.14, Y.25 Ligand excluded by PLIP NO3.12: 5 residues within 4Å: Chain A: Y.230, E.231, D.232, K.236 Ligands: NO3.18 Ligand excluded by PLIP NO3.13: 6 residues within 4Å: Chain A: M.62, K.238, G.263, H.264 Ligands: 3P3.3, NO3.20 Ligand excluded by PLIP NO3.14: 3 residues within 4Å: Chain A: V.137, E.138, Q.269 Ligand excluded by PLIP NO3.15: 4 residues within 4Å: Chain A: T.14, G.15, V.16, K.23 Ligand excluded by PLIP NO3.16: 6 residues within 4Å: Chain A: A.172, S.173, V.174, T.179, E.184, K.236 Ligand excluded by PLIP NO3.17: 5 residues within 4Å: Chain A: K.8, N.9, S.116, A.117, G.118 Ligand excluded by PLIP NO3.18: 5 residues within 4Å: Chain A: E.184, Y.230, E.231, K.236 Ligands: NO3.12 Ligand excluded by PLIP NO3.19: 3 residues within 4Å: Chain A: I.10, K.29, P.30 Ligand excluded by PLIP NO3.20: 10 residues within 4Å: Chain A: T.60, T.61, M.62, S.63, G.263, H.264, A.265, L.266 Ligands: NO3.13, NO3.21 Ligand excluded by PLIP NO3.21: 7 residues within 4Å: Chain A: E.139, K.142, G.263, H.264, A.265, L.266 Ligands: NO3.20 Ligand excluded by PLIP NO3.22: 5 residues within 4Å: Chain A: L.18, H.19, L.200, L.205, A.206 Ligand excluded by PLIP NO3.23: 5 residues within 4Å: Chain A: I.2, A.289, S.295, Y.296, M.297 Ligand excluded by PLIP NO3.24: 3 residues within 4Å: Chain A: Q.269, R.272, T.273 Ligand excluded by PLIP NO3.25: 5 residues within 4Å: Chain A: R.41, D.70, V.71, K.72, S.98 Ligand excluded by PLIP NO3.26: 2 residues within 4Å: Chain A: K.132, R.133 Ligand excluded by PLIP NO3.27: 4 residues within 4Å: Chain A: S.136, V.137, E.138, R.143 Ligand excluded by PLIP NO3.28: 6 residues within 4Å: Chain A: F.152, F.176, S.177, P.293, I.294, S.295 Ligand excluded by PLIP NO3.29: 2 residues within 4Å: Chain A: E.198, S.202 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C.J. et al., Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design. Chem.Biol. (2011)

Release Date

2011-01-05

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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