SMTL ID : 6y0v.1

Fucosylated bicyclic peptide bp71 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.7 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-4-3-mer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.2, ZDC.3 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.2: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: CA.1, ZDC.3 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.4: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain F: G.114 Ligands: CA.5, ZDC.6 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Metal complexes: C:N.21, C:D.101, C:D.104, F:G.114 CA.5: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: CA.4, ZDC.6 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.7: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.8, ZDC.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 CA.8: 7 residues within 4Å: Chain A: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: CA.7, ZDC.9 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Metal complexes: A:G.114, D:N.21, D:D.101, D:D.104 CA.10: 6 residues within 4Å: Chain F: E.95, D.99, D.101, D.104 Ligands: CA.11, ZDC.12 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.95, F:E.95, F:D.99, F:D.101, F:D.104 CA.11: 7 residues within 4Å: Chain C: G.114 Chain F: N.21, D.101, N.103, D.104 Ligands: CA.10, ZDC.12 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain C Metal complexes: F:N.21, F:D.101, F:D.101, F:D.104, C:G.114

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

ZDC.3: 12 residues within 4Å: Chain A: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Chain B: K.13 Chain D: G.114 Ligands: CA.1, CA.2 7 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:S.23, A:G.24, A:D.99, A:D.104, D:G.114 Water bridges: A:D.99 Hydrophobic interactions: B:K.13 ZDC.6: 13 residues within 4Å: Chain C: N.21, S.22, S.23, T.45, E.95, D.96, G.97, D.99, D.101, D.104 Chain F: G.114 Ligands: CA.4, CA.5 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:T.45 Hydrogen bonds: C:S.23, C:S.23, C:D.99, C:D.104, C:D.104, F:G.114 ZDC.9: 15 residues within 4Å: Chain A: G.114 Chain D: N.21, S.22, S.23, T.45, E.95, D.96, D.99, D.101, D.104 Chain E: K.6, K.9, K.13 Ligands: CA.7, CA.8 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:G.114, D:S.23, D:D.104 Hydrophobic interactions: D:T.45 ZDC.12: 14 residues within 4Å: Chain C: G.114 Chain F: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Chain G: K.6, K.9, K.13 Ligands: CA.10, CA.11 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:S.23, F:D.99, F:D.104, F:D.104, C:G.114 Water bridges: F:D.99

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: ACDF
bp71: BEG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

D
C

F
D

B
E

E
G

G
H

Fucose-binding lectin

bp71

Related Entries With Identical Sequence