SMTL ID : 6r35.1

Structure of the LecB lectin from Pseudomonas aeruginosa strain PAO1 in complex with lewis x tetrasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NAG-FUC-GAL.1: 14 residues within 4Å: Chain A: N.21, S.22, S.23, G.24, V.69, E.95, D.96, G.97, D.99, D.101, D.104 Chain D: G.114 Ligands: CA.5, CA.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.23, A:D.96, A:D.99, A:D.104, D:G.114, A:D.99, A:S.23, A:D.96 Water bridges: A:D.99, A:T.98, A:D.99, A:D.99, A:D.99 Hydrophobic interactions: A:V.69 NAG-FUC-GAL.2: 14 residues within 4Å: Chain A: G.114 Chain D: N.21, S.22, S.23, G.24, V.69, E.95, D.96, G.97, D.99, D.101, D.104 Ligands: CA.9, CA.18 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.23, D:D.96, D:D.99, D:D.101, D:D.99, D:S.23, D:D.96 Water bridges: D:D.99, D:D.99, D:T.98 Hydrophobic interactions: D:V.69 NAG-FUC-GAL.3: 15 residues within 4Å: Chain B: N.21, S.22, S.23, G.24, V.69, R.72, E.95, D.96, G.97, D.99, D.101, D.104 Chain C: G.114 Ligands: CA.10, CA.11 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.23, B:D.96, B:D.99, B:D.104, C:G.114, B:D.99, B:D.96 Water bridges: B:T.98, B:D.99, B:S.23 Hydrophobic interactions: B:V.69 NAG-FUC-GAL.4: 13 residues within 4Å: Chain B: G.114 Chain C: N.21, S.22, S.23, V.69, E.95, D.96, G.97, D.99, D.101, D.104 Ligands: CA.14, CA.15 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.23, C:D.96, C:D.99, B:G.114, C:D.99, C:D.96 Water bridges: C:T.98, C:T.98, C:D.99, C:S.23 Hydrophobic interactions: C:V.69

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.5: 7 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: NAG-FUC-GAL.1, CA.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Metal complexes: A:N.21, A:D.101, A:D.104, D:G.114 CA.6: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: NAG-FUC-GAL.1, CA.5 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.9: 7 residues within 4Å: Chain A: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: NAG-FUC-GAL.2, CA.18 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:N.21, D:D.101, D:D.104, A:G.114 CA.10: 7 residues within 4Å: Chain B: N.21, D.101, N.103, D.104 Chain C: G.114 Ligands: NAG-FUC-GAL.3, CA.11 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:N.21, B:D.101, B:D.104, C:G.114 CA.11: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: NAG-FUC-GAL.3, CA.10 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.14: 7 residues within 4Å: Chain B: G.114 Chain C: N.21, D.101, N.103, D.104 Ligands: NAG-FUC-GAL.4, CA.15 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Metal complexes: C:N.21, C:D.101, C:D.104, B:G.114 CA.15: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: NAG-FUC-GAL.4, CA.14 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.18: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: NAG-FUC-GAL.2, CA.9 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

2 x SO4: SULFATE ION(Non-covalent)

SO4.7: 3 residues within 4Å: Chain A: N.11, T.12, R.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.13 Water bridges: A:N.11 Salt bridges: A:R.13 SO4.19: 5 residues within 4Å: Chain D: Q.43, S.44, N.46, A.48 Ligands: EDO.20 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.44 Water bridges: D:N.46, D:N.46

8 x EDO: 1,2-ETHANEDIOL(Non-covalent)

EDO.8: 1 residues within 4Å: Chain A: S.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.59 EDO.12: 4 residues within 4Å: Chain B: S.44, T.45, N.46, A.48 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.45, B:N.46, B:N.46 Water bridges: B:Q.43, B:Q.43 EDO.13: 3 residues within 4Å: Chain B: N.33, G.58, S.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.33, B:S.59 EDO.16: 4 residues within 4Å: Chain C: V.32, N.33, G.58, S.59 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.32, C:N.33, C:S.59, C:S.59 EDO.17: 2 residues within 4Å: Chain C: L.55, N.56 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.56 EDO.20: 4 residues within 4Å: Chain D: Q.43, S.44, T.45 Ligands: SO4.19 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.43, D:S.44, D:T.45, D:N.46 EDO.21: 4 residues within 4Å: Chain D: A.37, A.38, T.39, Q.53 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.39, D:Q.53 EDO.22: 3 residues within 4Å: Chain D: P.73, S.74, D.75 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.75

Links

RCSB   PDBe   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

2019-06-12

Peptides

Fucose-binding lectin PA-IIL: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

Fucose-binding lectin PA-IIL

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