SMTL ID : 5a70.1

Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with lewis x tetrasaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x GAL- NAG- FUC- GAL: alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose

GAL-NAG-FUC-GAL.1: 15 residues within 4Å: Chain A: N.21, S.22, A.23, G.24, T.45, V.69, E.95, D.96, S.97, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.5, CA.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.45, A:V.69 Hydrogen bonds: A:A.23, A:D.96, A:D.99, A:D.101, A:D.99, A:A.23, A:S.97, A:S.97 Water bridges: A:S.97 GAL-NAG-FUC-GAL.2: 14 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, A.23, G.24, V.69, E.95, D.96, S.97, D.99, D.101, D.104 Ligands: CA.8, CA.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.23, B:D.96, B:D.99, B:D.104, A:G.114, B:D.99, B:S.97, B:S.97 Water bridges: B:S.97 Hydrophobic interactions: B:V.69 GAL-NAG-FUC-GAL.3: 13 residues within 4Å: Chain C: N.21, S.22, A.23, G.24, E.95, D.96, S.97, D.99, D.101, D.104 Chain D: G.114 Ligands: CA.10, CA.11 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.23, C:D.96, C:D.99, D:G.114, C:D.99, C:S.97, C:S.97 Water bridges: C:S.97 GAL-NAG-FUC-GAL.4: 14 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, A.23, G.24, T.45, E.95, D.96, S.97, D.99, D.101, D.104 Ligands: CA.13, CA.14 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:T.45 Hydrogen bonds: D:A.23, D:D.96, D:D.99, D:D.104, C:G.114, D:D.99, D:S.97, D:S.97 Water bridges: D:S.97, D:D.96

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: GAL-NAG-FUC-GAL.1, CA.6 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.6: 7 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain B: G.114 Ligands: GAL-NAG-FUC-GAL.1, CA.5 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.8: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: GAL-NAG-FUC-GAL.2, CA.9 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.9: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: GAL-NAG-FUC-GAL.2, CA.8 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Metal complexes: A:G.114, B:N.21, B:D.101, B:D.104 CA.10: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: GAL-NAG-FUC-GAL.3, CA.11 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.11: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: GAL-NAG-FUC-GAL.3, CA.10 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.13: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: GAL-NAG-FUC-GAL.4, CA.14 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.14: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: GAL-NAG-FUC-GAL.4, CA.13 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

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 2 residues within 4Å: Chain A: G.58, G.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.11, A:G.59 Water bridges: A:N.33, A:N.33, A:G.60 SO4.12: 3 residues within 4Å: Chain C: N.33, G.58, G.59 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.33, C:G.59 Water bridges: C:V.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lepsik, M. et al., Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study. Eur.J.Med.Chem. (2019)

Release Date

2016-07-27

Peptides

LECB: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

LECB

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