SMTL ID : 5a6y.1

Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with mannose-alpha1,3mannoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

3 x MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 12 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, A.23, E.95, D.96, S.97, D.99, D.101, D.104 Ligands: CA.8, CA.9 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.114, B:A.23, B:D.99, B:D.104 Water bridges: B:D.99 MAN-MAN.2: 12 residues within 4Å: Chain C: N.21, S.22, A.23, E.95, D.96, S.97, D.99, D.101, D.104 Chain D: G.114 Ligands: CA.10, CA.11 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:G.114, C:A.23, C:D.99, C:D.104, C:D.104 Water bridges: C:D.99, C:D.99 MAN-MAN.3: 12 residues within 4Å: Chain C: G.114 Chain D: N.21, S.22, A.23, E.95, D.96, S.97, D.99, D.101, D.104 Ligands: CA.13, CA.14 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.23, D:D.99, D:D.104, D:D.104, C:G.114 Water bridges: D:T.98

8 x CA: CALCIUM ION(Non-covalent)

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

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.6: 13 residues within 4Å: Chain A: N.21, S.22, A.23, E.95, D.96, S.97, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.4, CA.5, GOL.7 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.23, A:S.97, A:D.99, A:D.104, B:G.114 Water bridges: A:T.98

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 12 residues within 4Å: Chain A: N.21, S.22, E.95, D.96, S.97, D.99, D.101, D.104 Chain B: G.114 Ligands: CA.4, CA.5, MAN.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.96, A:D.99, B:G.114 Water bridges: A:T.98

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

SO4.12: 2 residues within 4Å: Chain C: E.35, T.36 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.36 Water bridges: C:Q.31, C:T.36, C:T.36, C:T.36, C:T.36

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

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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