SMTL ID : 8ano.1

Fucosylated mixed-chirality linear peptide FHP8 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.3 Angstrom resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 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 B: G.114 Ligands: CA.2, ZDC.10 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.2: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: CA.1, ZDC.10 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.3: 7 residues within 4Å: Chain A: G.114 Chain B: N.21, D.101, N.103, D.104 Ligands: CA.4, ZDC.5 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.4: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: CA.3, ZDC.5 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.6: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: CA.7, ZDC.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.7: 7 residues within 4Å: Chain C: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.6, ZDC.12 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.8: 7 residues within 4Å: Chain C: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: CA.9, ZDC.11 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 CA.9: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.8, ZDC.11 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

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Personne, H. et al., To Fold or Not to Fold: Diastereomeric Optimization of an alpha-Helical Antimicrobial Peptide. J.Med.Chem. (2023)

Release Date

2023-05-31

Peptides

Fucose-binding lectin PA-IIL: ABCD
Mixed-chirality fucosylated peptide FHP8: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
H

G
I

Fucose-binding lectin PA-IIL

Mixed-chirality fucosylated peptide FHP8

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