SMTL ID : 6uec.1

Pseudomonas aeruginosa LpxD Complex Structure with Ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

3 x Q5M: 4-(naphthalen-1-yl)-4-oxobutanoic acid(Non-covalent)

Q5M.1: 13 residues within 4Å: Chain A: M.255, G.273, S.275, G.291, L.292, V.293, G.294, M.309 Chain C: A.269, A.287, G.288, G.306 Ligands: DMS.8 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.293 Hydrogen bonds: A:S.275, A:S.275, A:G.294, C:G.288 Q5M.4: 13 residues within 4Å: Chain A: A.269, A.287, G.288, G.306 Chain B: M.255, G.273, S.275, G.291, L.292, V.293, G.294, M.309 Ligands: DMS.2 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.293 Hydrogen bonds: B:S.275, B:S.275, B:G.294, A:G.288 Q5M.7: 13 residues within 4Å: Chain B: A.269, A.287, G.288, G.306 Chain C: M.255, G.273, S.275, G.291, L.292, V.293, G.294, M.309 Ligands: DMS.5 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.293 Hydrogen bonds: C:S.275, C:S.275, C:G.294, B:G.288

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 8 residues within 4Å: Chain A: C.271, M.307 Chain B: C.271, G.273, G.289, V.290, G.291 Ligands: Q5M.4 No protein-ligand interaction detected (PLIP) DMS.5: 8 residues within 4Å: Chain B: C.271, M.307 Chain C: C.271, G.273, G.289, V.290, G.291 Ligands: Q5M.7 No protein-ligand interaction detected (PLIP) DMS.8: 8 residues within 4Å: Chain A: C.271, G.273, G.289, V.290, G.291 Chain C: C.271, M.307 Ligands: Q5M.1 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 2 residues within 4Å: Ligands: MG.6, MG.9 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Ligands: MG.3, MG.9 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Ligands: MG.3, MG.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kroeck, K.G. et al., Discovery of dual-activity small-molecule ligands of Pseudomonas aeruginosa LpxA and LpxD using SPR and X-ray crystallography. Sci Rep (2019)

Release Date

2019-11-13

Peptides

UDP-3-O-acylglucosamine N-acyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

UDP-3-O-acylglucosamine N-acyltransferase