SMTL ID : 3dcq.1

LECB (PA-LII) in complex with the synthetic ligand 2G0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: E.95, D.96, D.99, D.101, D.104 Ligands: CA.2, 2G0.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.95, A:E.95, A:D.99, A:D.101, A:D.104 CA.2: 7 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain B: G.114 Ligands: CA.1, 2G0.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:N.21, A:D.101, A:D.104, B:G.114 CA.4: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: CA.5, 2G0.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.95, B:E.95, B:D.99, B:D.101, B:D.104 CA.5: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: CA.4, 2G0.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:N.21, B:D.101, B:D.104, A:G.114 CA.7: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.8, 2G0.9 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:N.21, C:D.101, C:D.104, D:G.114 CA.8: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: CA.7, 2G0.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.95, C:E.95, C:D.99, C:D.101, C:D.104 CA.10: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.11, 2G0.12 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.95, D:E.95, D:D.99, D:D.101, D:D.104 CA.11: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: CA.10, 2G0.12 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Metal complexes: D:N.21, D:D.101, D:D.104, C:G.114

4 x 2G0: (2S)-1-[(2S)-6-amino-2-({[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl]acetyl}amino)hexanoyl]-N-[(1S)-1-carbamoyl-3-methylbutyl]pyrrolidine-2-carboxamide(Non-covalent)

2G0.3: 14 residues within 4Å: Chain A: N.21, S.22, S.23, G.24, T.45, N.70, E.95, D.96, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.1, CA.2 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.45, A:D.96 Hydrogen bonds: A:S.23, A:S.23, A:N.70, A:N.70, A:D.96, A:D.104, B:G.114 2G0.6: 13 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, S.23, T.45, E.95, D.96, G.97, D.99, D.101, D.104 Ligands: CA.4, CA.5 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.45 Hydrogen bonds: B:S.23, B:S.23, B:D.96, B:D.104, A:G.114 Water bridges: B:E.95, B:D.99 2G0.9: 12 residues within 4Å: Chain C: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Chain D: G.114 Ligands: CA.7, CA.8 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.23, C:S.23, C:D.96, C:D.101, D:G.114 Water bridges: C:D.99 2G0.12: 13 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, S.23, T.45, E.95, D.96, G.97, D.99, D.101, D.104 Ligands: CA.10, CA.11 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:T.45 Hydrogen bonds: D:S.23, D:D.96, D:D.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, E.M. et al., Inhibition and dispersion of Pseudomonas aeruginosa biofilms by glycopeptide dendrimers targeting the fucose-specific lectin LecB. Chem.Biol. (2008)

Release Date

2009-01-13

Peptides

Fucose-binding lectin PA-IIL: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fucose-binding lectin PA-IIL

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