SMTL ID : 4lke.1

Crystal Structure of Pseudomonas aeruginosa Lectin LecA Complexed with GalA-WRI at 1.65 A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

4 x TRP- ARG- ILE: peptide WRIA(Non-functional Binders)(Non-covalent)

TRP-ARG-ILE.1: 1 residues within 4Å: Ligands: PHB.13 No protein-ligand interaction detected (PLIP) TRP-ARG-ILE.2: 4 residues within 4Å: Chain D: E.49, P.51, Q.53 Ligands: PHB.14 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:P.51 Hydrogen bonds: D:Q.53, D:Q.53 TRP-ARG-ILE.3: 3 residues within 4Å: Chain B: P.51, Q.53 Ligands: PHB.15 No protein-ligand interaction detected (PLIP) TRP-ARG-ILE.4: 1 residues within 4Å: Ligands: PHB.16 Protein-ligand interaction information (PLIP) not available

4 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.5: 9 residues within 4Å: Chain A: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.6, PHB.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.100, A:N.107 Water bridges: A:H.50, A:P.51, A:N.107 GAL.7: 9 residues within 4Å: Chain B: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.8, PHB.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.100, B:T.104, B:N.107 Water bridges: B:P.51, B:N.107 GAL.9: 9 residues within 4Å: Chain C: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.10, PHB.16 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.100, C:T.104, C:N.107 Water bridges: C:H.50, C:P.51, C:T.104, C:N.107 GAL.11: 9 residues within 4Å: Chain D: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.12, PHB.14 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.100, D:N.107 Water bridges: D:H.50, D:Q.53, D:Q.53, D:T.104, D:N.107

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: Y.36, D.100, T.104, N.107, N.108 Ligands: GAL.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.36, A:D.100, A:T.104 CA.8: 6 residues within 4Å: Chain B: Y.36, D.100, T.104, N.107, N.108 Ligands: GAL.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.36, B:D.100, B:T.104 CA.10: 6 residues within 4Å: Chain C: Y.36, D.100, T.104, N.107, N.108 Ligands: GAL.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:Y.36, C:D.100, C:T.104 CA.12: 6 residues within 4Å: Chain D: Y.36, D.100, T.104, N.107, N.108 Ligands: GAL.11 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:Y.36, D:D.100, D:T.104

4 x PHB: P-HYDROXYBENZOIC ACID(Non-covalent)

PHB.13: 5 residues within 4Å: Chain A: Y.36, P.38, H.50 Ligands: TRP-ARG-ILE.1, GAL.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.38 pi-Stacking: A:H.50 PHB.14: 5 residues within 4Å: Chain D: Y.36, H.50 Ligands: TRP-ARG-ILE.2, TRP-ARG-ILE.2, GAL.11 1 PLIP interactions: 1 interactions with chain D pi-Stacking: D:H.50 PHB.15: 5 residues within 4Å: Chain B: Y.36, P.38, H.50 Ligands: TRP-ARG-ILE-ALA.3, GAL.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.36, B:P.38 pi-Stacking: B:H.50 PHB.16: 4 residues within 4Å: Chain C: Y.36, H.50 Ligands: TRP.4, GAL.9 1 PLIP interactions: 1 interactions with chain C pi-Stacking: C:H.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadam, R.U. et al., Structure-Based Optimization of the Terminal Tripeptide in Glycopeptide Dendrimer Inhibitors of Pseudomonas aeruginosa Biofilms Targeting LecA. Chemistry (2013)

Release Date

2013-12-18

Peptides

PA-I galactophilic lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PA-I galactophilic lectin

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