SMTL ID : 2ves.1

Crystal Structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.78, H.237, D.241 Ligands: GVR.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.78, A:H.237, A:D.241, A:D.241 ZN.3: 4 residues within 4Å: Chain A: D.159, D.161 Chain B: H.162, E.219 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:D.159, A:D.161, B:H.162, B:E.219, B:E.219 ZN.4: 4 residues within 4Å: Chain B: H.78, H.237, D.241 Ligands: GVR.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.78, B:H.237, B:D.241, B:D.241 ZN.6: 4 residues within 4Å: Chain B: D.159, D.161 Chain C: H.162, E.219 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Metal complexes: C:H.162, C:E.219, B:D.159, B:D.161, B:D.161 ZN.8: 4 residues within 4Å: Chain C: H.78, H.237, D.241 Ligands: GVR.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.78, C:H.237, C:D.241, C:D.241 ZN.10: 4 residues within 4Å: Chain A: H.162, E.219 Chain C: D.159, D.161 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Metal complexes: A:H.162, A:E.219, A:E.219, C:D.159, C:D.161 ZN.11: 3 residues within 4Å: Chain A: Q.203 Chain C: E.134, S.136 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.134, C:S.136, H2O.47, H2O.47, H2O.47

3 x GVR: (2R)-N-hydroxy-3-naphthalen-2-yl-2-[(naphthalen-2-ylsulfonyl)amino]propanamide

GVR.2: 22 residues within 4Å: Chain A: L.18, M.62, S.63, T.75, E.77, H.78, I.102, T.190, F.191, G.192, F.193, D.196, I.197, L.200, G.209, S.210, N.213, A.214, H.237, D.241, H.264 Ligands: ZN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.18, A:L.18, A:D.196, A:I.197, A:I.197, A:L.200, A:A.214 Hydrogen bonds: A:M.62, A:M.62, A:T.190 Water bridges: A:S.63 GVR.5: 21 residues within 4Å: Chain B: L.18, M.62, S.63, E.77, H.78, I.102, T.190, F.191, G.192, F.193, D.196, I.197, L.200, G.209, S.210, N.213, A.214, H.237, D.241, H.264 Ligands: ZN.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.18, B:L.18, B:D.196, B:I.197, B:I.197, B:L.200, B:A.214 Hydrogen bonds: B:M.62, B:M.62, B:E.77, B:T.190 GVR.9: 19 residues within 4Å: Chain C: L.18, M.62, S.63, E.77, H.78, I.102, T.190, F.191, G.192, D.196, I.197, G.209, S.210, N.213, A.214, H.237, D.241, H.264 Ligands: ZN.8 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.18, C:L.18, C:D.196, C:I.197, C:A.214 Hydrogen bonds: C:M.62, C:M.62, C:E.77

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

SO4.7: 1 residues within 4Å: Chain B: T.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.14 Water bridges: B:T.14, B:T.14 Salt bridges: B:K.23 SO4.12: 4 residues within 4Å: Chain C: M.1, E.287, D.288, A.289 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:M.1, C:M.1, C:D.288, C:A.289 Water bridges: C:D.288, C:D.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mochalkin, I. et al., Crystal structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor. Protein Sci. (2008)

Release Date

2008-01-15

Peptides

UDP-3-O-acyl-N-acetylglucosamine deacetylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

UDP-3-O-acyl-N-acetylglucosamine deacetylase

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