SMTL ID : 5a6z.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

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

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

NAG-GAL-FUC.2: 14 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, A.23, G.24, T.45, E.95, D.96, S.97, D.99, D.101, D.104 Ligands: CA.8, CA.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.45 Hydrogen bonds: B:A.23, B:D.96, B:D.99, A:G.114, B:D.99, B:S.22, B:G.24 Water bridges: B:T.98, B:T.98, B:D.99, B:S.22, B:S.97

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

GAL-NAG-GAL-FUC.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.11, CA.12 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.114, C:A.23, C:D.96, C:D.99, C:D.99, C:S.22, C:G.24, C:S.97 Water bridges: C:T.98, C:T.98, C:S.22

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: GLA-NAG-GAL-FUC.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: GLA-NAG-GAL-FUC.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: NAG-GAL-FUC.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: NAG-GAL-FUC.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.11: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: GAL-NAG-GAL-FUC.3, CA.12 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.12: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: GAL-NAG-GAL-FUC.3, CA.11 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.14: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: GLA-NAG-GAL-FUC.4, CA.15 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.15: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: GLA-NAG-GAL-FUC.4, CA.14 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

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

SO4.7: 3 residues within 4Å: Chain A: S.44, N.46, A.48 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.44, A:N.46 Water bridges: A:T.45, A:N.46 SO4.10: 2 residues within 4Å: Chain B: G.58, G.59 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.11, B:G.59 Water bridges: B:N.33, B:G.60 SO4.13: 4 residues within 4Å: Chain C: V.32, N.33, G.58, G.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.33, C:G.59

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

PEG.16: 4 residues within 4Å: Chain D: S.44, T.45, N.46, A.48 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.45, D:T.45, D:N.46 Water bridges: D:Q.43, D:Q.43, D:N.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sommer, R. et al., The virulence factor LecB varies in clinical isolates: consequences for ligand binding and drug discovery. Chem Sci (2016)

Release Date

2016-05-25

Peptides

LECB: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

LECB

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