SMTL ID : 8r1b.1

Crystal structure of recombinant LasB from Pseudomonas aeruginosa PAO1 in complex with 6466

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.338, H.342, Y.353, E.362 Ligands: XI5.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.338, A:H.342, A:E.362

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.334, E.370, E.373, D.381, L.383, I.384 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.334, A:E.370, A:E.373, A:L.383, H2O.2

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: D.218, Y.219, R.377, K.379 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.377 Water bridges: A:D.218, A:K.379 GOL.4: 6 residues within 4Å: Chain A: D.239, K.248, T.250, P.251, F.252, R.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.248, A:R.253, A:R.253 GOL.5: 6 residues within 4Å: Chain A: T.249, Y.299, K.301, D.314, T.316, A.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.301, A:D.314 Water bridges: A:D.246

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.6: 2 residues within 4Å: Chain A: N.416, G.417 No protein-ligand interaction detected (PLIP)

1 x XI5: [(2~{S})-1-[[1-[(4-ethanoylphenyl)amino]-3-methyl-1-oxidanylidene-butan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]phosphonic acid(Non-covalent)

XI5.7: 14 residues within 4Å: Chain A: A.311, F.327, V.335, H.338, E.339, H.342, Y.353, E.362, D.366, I.384, L.395, R.396, H.421 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.395 Hydrogen bonds: A:Y.353, A:R.396, A:R.396 Water bridges: A:N.310, A:A.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolling, D. et al., Dipeptidic Phosphonates: Potent Inhibitors of Pseudomonas aeruginosa Elastase B Showing Efficacy in a Murine Keratitis Model. Chemrxiv (2024)

Release Date

2024-10-16

Peptides

Pro-elastase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pro-elastase

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