SMTL ID : 7nef.1

Fucosylated linear peptide Fln65 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.5 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

hetero-8-8-mer

Ligands

16 x CA: CALCIUM ION(Non-covalent)

CA.1: 8 residues within 4Å: Chain A: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: CA.2, ZDC.17 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: 8 residues within 4Å: Chain A: N.22, S.23, D.102, N.104, D.105 Chain B: G.115 Ligands: CA.1, ZDC.17 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.3: 8 residues within 4Å: Chain B: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: CA.4, ZDC.18 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.4: 8 residues within 4Å: Chain A: G.115 Chain B: N.22, S.23, D.102, N.104, D.105 Ligands: CA.3, ZDC.18 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.5: 8 residues within 4Å: Chain C: N.22, S.23, D.102, N.104, D.105 Chain D: G.115 Ligands: CA.6, ZDC.19 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Metal complexes: D:G.115, C:N.22, C:D.102, C:D.105 CA.6: 8 residues within 4Å: Chain C: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: CA.5, ZDC.19 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.7: 8 residues within 4Å: Chain C: G.115 Chain D: N.22, S.23, D.102, N.104, D.105 Ligands: CA.8, ZDC.20 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Metal complexes: C:G.115, D:N.22, D:D.102, D:D.105 CA.8: 8 residues within 4Å: Chain D: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: CA.7, ZDC.20 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.9: 8 residues within 4Å: Chain E: N.22, S.23, D.102, N.104, D.105 Chain F: G.115 Ligands: CA.10, ZDC.21 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Metal complexes: E:N.22, E:D.102, E:D.105, F:G.115 CA.10: 8 residues within 4Å: Chain E: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: CA.9, ZDC.21 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.11: 9 residues within 4Å: Chain F: E.96, D.97, D.100, N.101, D.102, Y.103, D.105 Ligands: CA.12, ZDC.22 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.12: 8 residues within 4Å: Chain E: G.115 Chain F: N.22, S.23, D.102, N.104, D.105 Ligands: CA.11, ZDC.22 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Metal complexes: F:N.22, F:D.102, F:D.105, E:G.115 CA.13: 8 residues within 4Å: Chain G: N.22, S.23, D.102, N.104, D.105 Chain H: G.115 Ligands: CA.14, ZDC.23 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain G Metal complexes: H:G.115, G:N.22, G:D.102, G:D.105 CA.14: 8 residues within 4Å: Chain G: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: CA.13, ZDC.23 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.96, G:E.96, G:D.100, G:D.102, G:D.105 CA.15: 10 residues within 4Å: Chain H: E.96, D.97, G.98, D.100, N.101, D.102, Y.103, D.105 Ligands: CA.16, ZDC.24 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.96, H:E.96, H:D.100, H:D.102, H:D.105 CA.16: 8 residues within 4Å: Chain G: G.115 Chain H: N.22, S.23, D.102, N.104, D.105 Ligands: CA.15, ZDC.24 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G Metal complexes: H:N.22, H:D.102, H:D.105, G:G.115

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

ZDC.17: 17 residues within 4Å: Chain A: N.22, S.23, S.24, G.25, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain B: G.115 Chain I: K.1, K.2, K.5 Ligands: CA.1, CA.2 6 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A, 1 interactions with chain I Hydrogen bonds: B:G.115, A:S.24, A:D.102, A:D.105 Water bridges: A:G.25, I:K.5 ZDC.18: 16 residues within 4Å: Chain A: G.115 Chain B: N.22, S.23, S.24, G.25, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain J: K.1, K.2 Ligands: CA.3, CA.4 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.115, B:S.24, B:D.102, B:D.105, B:D.105 Hydrophobic interactions: B:T.46 ZDC.19: 16 residues within 4Å: Chain C: N.22, S.23, S.24, G.25, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain D: G.115 Chain K: K.1, K.2 Ligands: CA.5, CA.6 7 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: C:T.46 Hydrogen bonds: C:S.24, C:D.102, C:D.105, D:G.115 Water bridges: K:K.2, K:K.2 ZDC.20: 16 residues within 4Å: Chain C: G.115 Chain D: N.22, S.23, S.24, G.25, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain L: K.1, K.2 Ligands: CA.7, CA.8 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.24, D:D.102, D:D.105, D:D.105, C:G.115 Water bridges: D:S.23 ZDC.21: 16 residues within 4Å: Chain E: N.22, S.23, S.24, G.25, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain F: G.115 Chain M: K.1, K.2 Ligands: CA.9, CA.10 9 PLIP interactions: 1 interactions with chain F, 7 interactions with chain E, 1 interactions with chain M Hydrogen bonds: F:G.115, E:S.24, E:S.24, E:D.97, E:D.102, E:D.105 Hydrophobic interactions: E:T.46, M:K.1 Water bridges: E:S.23 ZDC.22: 16 residues within 4Å: Chain E: G.115 Chain F: N.22, S.23, S.24, G.25, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain N: K.1, K.2 Ligands: CA.11, CA.12 9 PLIP interactions: 1 interactions with chain E, 6 interactions with chain F, 2 interactions with chain N Hydrogen bonds: E:G.115, F:S.24, F:G.25, F:D.97, F:D.102, N:K.2 Water bridges: F:S.23, F:D.100, N:K.2 ZDC.23: 16 residues within 4Å: Chain G: N.22, S.23, S.24, G.25, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain H: G.115 Chain O: K.1, K.2 Ligands: CA.13, CA.14 9 PLIP interactions: 6 interactions with chain G, 2 interactions with chain O, 1 interactions with chain H Hydrophobic interactions: G:T.46, O:K.1 Hydrogen bonds: G:S.24, G:D.100, G:D.105, G:D.105, H:G.115 Water bridges: G:G.25, O:K.2 ZDC.24: 17 residues within 4Å: Chain G: G.115 Chain H: N.22, S.23, S.24, G.25, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain P: K.1, K.2, K.5 Ligands: CA.15, CA.16 7 PLIP interactions: 1 interactions with chain P, 5 interactions with chain H, 1 interactions with chain G Hydrogen bonds: P:K.2, H:S.24, H:D.102, H:D.105, G:G.115 Hydrophobic interactions: H:T.46 Water bridges: H:G.25

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

2021-03-03

Peptides

Fucose-binding lectin: ABCDEFGH
Fln65: IJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Fucose-binding lectin

Fln65

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