SMTL ID : 7psy.1

X-ray crystal structure of perdeuterated LecB lectin in complex with perdeuterated fucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.90 Å

Oligo State

homo-tetramer

Ligands

4 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.1: 13 residues within 4Å: Chain A: N.22, S.23, S.24, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain B: G.115 Ligands: CA.2, CA.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.24, A:D.97, B:G.115 Water bridges: A:S.24, A:G.25, A:E.96, A:D.97 FUC.5: 13 residues within 4Å: Chain A: G.115 Chain B: N.22, S.23, S.24, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Ligands: CA.7, CA.8 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.24, B:D.97, A:G.115 Water bridges: B:E.96, B:D.97 FUC.9: 13 residues within 4Å: Chain C: N.22, S.23, S.24, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain D: G.115 Ligands: CA.10, CA.11 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.46 Hydrogen bonds: C:S.24, C:D.97, D:G.115 Water bridges: C:E.96, C:D.97, C:D.100 FUC.12: 13 residues within 4Å: Chain C: G.115 Chain D: N.22, S.23, S.24, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Ligands: CA.13, CA.14 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.24, D:S.24, D:D.97, D:D.105, C:G.115 Water bridges: D:E.96, D:D.97, D:D.100

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 8 residues within 4Å: Chain A: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: FUC.1, CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.96, A:E.96, A:D.100, A:D.102, A:D.105 CA.3: 8 residues within 4Å: Chain A: N.22, S.23, D.102, N.104, D.105 Chain B: G.115 Ligands: FUC.1, CA.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:N.22, A:D.102, A:D.105, B:G.115 CA.7: 8 residues within 4Å: Chain A: G.115 Chain B: N.22, S.23, D.102, N.104, D.105 Ligands: FUC.5, CA.8 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:N.22, B:D.102, B:D.105, A:G.115 CA.8: 8 residues within 4Å: Chain B: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: FUC.5, CA.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.96, B:E.96, B:D.100, B:D.102, B:D.105 CA.10: 8 residues within 4Å: Chain C: N.22, S.23, D.102, N.104, D.105 Chain D: G.115 Ligands: FUC.9, CA.11 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:N.22, C:D.102, C:D.105, D:G.115 CA.11: 8 residues within 4Å: Chain C: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: FUC.9, CA.10 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.96, C:E.96, C:D.100, C:D.102, C:D.105 CA.13: 8 residues within 4Å: Chain D: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: FUC.12, CA.14 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.96, D:E.96, D:D.100, D:D.102, D:D.105 CA.14: 8 residues within 4Å: Chain C: G.115 Chain D: N.22, S.23, D.102, N.104, D.105 Ligands: FUC.12, CA.13 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Metal complexes: D:N.22, D:D.102, D:D.105, C:G.115

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

SO4.4: 3 residues within 4Å: Chain A: N.12, T.13, R.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.14 Salt bridges: A:R.14 SO4.6: 5 residues within 4Å: Chain B: Q.44, S.45, T.46, N.47, A.49 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.45, B:N.47 Water bridges: B:N.47, B:N.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gajdos, L. et al., Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding. Nat Commun (2022)

Release Date

2022-01-12

Peptides

Fucose-binding lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fucose-binding lectin

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