SMTL ID : 4cpb.1 (2 other biounits)

CRYSTAL STRUCTURE OF LECA IN COMPLEX WITH A DIVALENT GALACTOSIDE AT 1. 57 ANGSTROM IN MAGNESIUM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: Y.36, D.100, T.104, N.107, N.108 Ligands: GAL.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.36, A:D.100, A:T.104 CA.5: 6 residues within 4Å: Chain B: Y.36, D.100, T.104, N.107, N.108 Ligands: GAL.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.36, B:D.100, B:T.104 CA.9: 6 residues within 4Å: Chain C: Y.36, D.100, T.104, N.107, N.108 Ligands: GAL.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:Y.36, C:D.100, C:T.104 CA.13: 6 residues within 4Å: Chain D: Y.36, D.100, T.104, N.107, N.108 Ligands: GAL.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:Y.36, D:D.100, D:T.104

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

GAL.2: 9 residues within 4Å: Chain A: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.1, CN8.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.104, A:N.107 Water bridges: A:T.104 GAL.6: 9 residues within 4Å: Chain B: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.5, CN8.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.104, B:T.104, B:N.107 Water bridges: B:H.50 GAL.10: 9 residues within 4Å: Chain C: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.9, CN8.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.104, C:N.107 Water bridges: C:H.50, C:P.51 GAL.14: 9 residues within 4Å: Chain D: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.13, CN8.15 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.100, D:N.107 Water bridges: D:H.50, D:P.51, D:T.104, D:T.104, D:G.106

4 x CN8: (4S)-N-ethyl-4-{[N-methyl-3-(1-{2-[(4-sulfanylbenzoyl)amino]ethyl}-1H-1,2,3-triazol-4-yl)-L-alanyl]amino}-L-prolinamide(Non-covalent)

CN8.3: 6 residues within 4Å: Chain A: Y.36, P.38, H.50, P.51, Q.53 Ligands: GAL.2 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.50 CN8.7: 6 residues within 4Å: Chain B: Y.36, E.49, H.50, P.51, Q.53 Ligands: GAL.6 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:H.50 CN8.11: 6 residues within 4Å: Chain C: Y.36, E.49, H.50, P.51, Q.53 Ligands: GAL.10 1 PLIP interactions: 1 interactions with chain C pi-Stacking: C:H.50 CN8.15: 5 residues within 4Å: Chain D: Y.36, H.50, P.51, Q.53 Ligands: GAL.14 1 PLIP interactions: 1 interactions with chain D pi-Stacking: D:H.50

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: E.11, A.12, I.56, K.68, I.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.12, A:K.68

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 3 residues within 4Å: Chain B: A.12, K.68, I.97 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.12, B:K.68

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.12: 10 residues within 4Å: Chain D: E.11, A.12, I.56, K.68, G.70, N.71, S.72, G.73, T.95, I.97 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.68, D:N.71 Water bridges: D:T.74

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 3 residues within 4Å: Chain D: L.7, N.10, Q.14 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Novoa, A. et al., A Leca Ligand Identified from a Galactoside-Conjugate Array Inhibits Host Cell Invasion by Pseudomonas Aeruginosa. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-10-08

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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