SMTL ID : 6y0u.1

Fucosylated Bicyclic peptide bp71 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.5 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

hetero-4-3-mer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.96, D.100, D.102, D.105 Ligands: CA.2, ZDC.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.2: 7 residues within 4Å: Chain A: N.22, D.102, N.104, D.105 Chain C: G.115 Ligands: CA.1, ZDC.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:N.22, A:D.102, A:D.105, C:G.115 CA.4: 6 residues within 4Å: Chain C: E.96, D.100, D.102, D.105 Ligands: CA.5, ZDC.6 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.5: 7 residues within 4Å: Chain A: G.115 Chain C: N.22, D.102, N.104, D.105 Ligands: CA.4, ZDC.6 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:N.22, C:D.102, C:D.105, A:G.115 CA.7: 6 residues within 4Å: Chain E: E.96, D.100, D.102, D.105 Ligands: CA.8, ZDC.9 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.96, E:E.96, E:D.100, E:D.102, E:D.105 CA.8: 7 residues within 4Å: Chain E: N.22, D.102, N.104, D.105 Chain F: G.115 Ligands: CA.7, ZDC.9 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Metal complexes: F:G.115, E:N.22, E:D.102, E:D.105 CA.10: 6 residues within 4Å: Chain F: E.96, D.100, D.102, D.105 Ligands: CA.11, ZDC.12 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.96, F:E.96, F:D.100, F:D.102, F:D.105 CA.11: 7 residues within 4Å: Chain E: G.115 Chain F: N.22, D.102, N.104, D.105 Ligands: CA.10, ZDC.12 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F Metal complexes: E:G.115, F:N.22, F:D.102, F:D.105

4 x ZDC: 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid(Post Translational Modification)(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baeriswyl, S. et al., A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography. Rsc Chem Biol (2021)

Release Date

2021-02-24

Peptides

Fucose-binding lectin: ACEF
bp71: BDG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

F
D

B
E

D
F

G
H

Fucose-binding lectin

bp71

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