SMTL ID : 4lkd.1 (1 other biounit)

Crystal Structure of Pseudomonas aeruginosa Lectin LecA Complexed with GalA-QRS at 2.31 A Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-tetramer

Ligands

4 x GLN- ARG- SER- ALA: peptide QRSA(Non-covalent)

GLN-ARG-SER-ALA.1: 3 residues within 4Å: Chain A: P.51, Q.53 Ligands: PHB.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.53 Water bridges: A:H.50 GLN-ARG-SER-ALA.2: 3 residues within 4Å: Chain B: P.51, Q.53 Ligands: PHB.14 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.50 GLN-ARG-SER-ALA.3: 3 residues within 4Å: Chain C: P.51, Q.53 Ligands: PHB.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.51 Hydrogen bonds: C:Q.53 Water bridges: C:Q.53 GLN-ARG-SER-ALA.4: 4 residues within 4Å: Chain D: E.49, P.51, Q.53 Ligands: PHB.16 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.51 Hydrogen bonds: D:Q.53 Water bridges: D:E.49 Salt bridges: D:E.49

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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.104, A:T.104, A:N.107 Water bridges: A:H.50, A:Q.53, A:T.104, 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.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.100, B:N.107 Water bridges: B:H.50, B:Q.53 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.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.107 Water bridges: C:P.51, C:Q.53 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.16 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.104, D:T.104, D:N.107 Water bridges: D:P.51

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: 6 residues within 4Å: Chain A: Y.36, H.50 Ligands: GLN-ARG-SER-ALA.1, GLN-ARG-SER-ALA.1, GLN-ARG-SER-ALA.1, GAL.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.50, A:N.107 pi-Stacking: A:H.50 PHB.14: 6 residues within 4Å: Chain B: Y.36, H.50, Q.53 Ligands: GLN-ARG.2, GLN-ARG.2, GAL.7 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.107 pi-Stacking: B:H.50 PHB.15: 5 residues within 4Å: Chain C: Y.36, H.50 Ligands: GLN-ARG-SER-ALA.3, GLN-ARG-SER-ALA.3, GAL.9 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.107 pi-Stacking: C:H.50 PHB.16: 4 residues within 4Å: Chain D: Y.36, H.50 Ligands: GLN-ARG-SER.4, GAL.11 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.107 pi-Stacking: D: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
C

C
D

D
E

PA-I galactophilic lectin

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