SMTL ID : 8an9.1

Fucosylated mixed-chirality linear peptide FHP5 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 1.27 Å

Oligo State

hetero-4-3-mer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

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

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

ZDC.7: 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 D: G.114 Ligands: CA.5, CA.6 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.45 Hydrogen bonds: C:S.23, C:D.99, C:D.104, D:G.114 Water bridges: C:G.24, C:D.99 ZDC.10: 17 residues within 4Å: Chain A: N.21, S.22, S.23, T.45, E.95, D.96, G.97, D.99, D.101, D.104 Chain B: G.114 Chain E: K.1, K.2, L.3, L.4 Ligands: CA.1, CA.2 10 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 4 interactions with chain E Hydrophobic interactions: A:T.45, E:L.3, E:L.4 Hydrogen bonds: A:S.23, A:S.23, A:D.99, A:D.104, B:G.114, E:L.3, E:L.4 ZDC.11: 15 residues within 4Å: Chain A: G.114 Chain B: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Chain F: K.1, K.2, L.3, L.4 Ligands: CA.3, CA.4 9 PLIP interactions: 4 interactions with chain F, 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: F:L.3, F:L.4 Hydrogen bonds: F:L.3, F:L.4, A:G.114, B:S.23, B:D.99, B:D.104, B:D.104 ZDC.12: 13 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 G: K.1 Ligands: CA.8, CA.9 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.23, D:S.23, D:D.99, D:D.104, D:D.104, C:G.114 Water bridges: D: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 peptide FHP5: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Fucose-binding lectin PA-IIL

Mixed-chirality peptide FHP5

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