SMTL ID : 6s5r.1

Cfucosylated second generation peptide dendrimer SBD6 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 2.08 Angstrom resolution, incomplete structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-tetramer

Ligands

2 x DPP: SBD6(Non-covalent)

DPP.1: 2 residues within 4Å: Chain B: S.24 Ligands: ZDC.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.24 DPP.2: 3 residues within 4Å: Chain D: R.73, D.97 Ligands: ZDC.14 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: E.96, D.100, D.102, D.105 Ligands: CA.4, ZDC.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.96, A:D.100, A:D.102, A:D.105, A:D.105 CA.4: 7 residues within 4Å: Chain A: N.22, D.102, N.104, D.105 Chain B: G.115 Ligands: CA.3, ZDC.5 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.6: 7 residues within 4Å: Chain A: G.115 Chain B: N.22, D.102, N.104, D.105 Ligands: ZDC.7, CA.8 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Metal complexes: A:G.115, B:N.22, B:D.102, B:D.105 CA.8: 7 residues within 4Å: Chain B: E.96, D.97, D.100, D.102, D.105 Ligands: CA.6, ZDC.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.96, B:D.100, B:D.102, B:D.105, B:D.105 CA.9: 6 residues within 4Å: Chain C: E.96, D.100, D.102, D.105 Ligands: CA.10, ZDC.11 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.10: 7 residues within 4Å: Chain C: N.22, D.102, N.104, D.105 Chain D: G.115 Ligands: CA.9, ZDC.11 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:N.22, C:D.102, C:D.105, D:G.115 CA.12: 7 residues within 4Å: Chain C: G.115 Chain D: N.22, D.102, N.104, D.105 Ligands: CA.13, ZDC.14 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Metal complexes: D:N.22, D:D.102, D:D.105, C:G.115 CA.13: 6 residues within 4Å: Chain D: E.96, D.100, D.102, D.105 Ligands: CA.12, ZDC.14 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

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

ZDC.5: 12 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: G.115 Ligands: CA.3, CA.4 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.24, A:S.24, A:D.100, A:D.105, A:D.105, B:G.115 Water bridges: A:D.100 ZDC.7: 13 residues within 4Å: Chain A: G.115 Chain B: N.22, S.23, S.24, E.96, D.97, G.98, D.100, D.102, D.105 Ligands: DPP.1, CA.6, CA.8 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.24, B:D.105, B:D.105, A:G.115 Water bridges: B:D.100 ZDC.11: 12 residues within 4Å: Chain C: N.22, S.23, S.24, T.46, E.96, D.97, D.100, D.102, D.105 Chain D: G.115 Ligands: CA.9, CA.10 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.115, C:S.24, C:D.100, C:D.105 Hydrophobic interactions: C:T.46 ZDC.14: 13 residues within 4Å: Chain C: G.115 Chain D: N.22, S.23, S.24, E.96, D.97, D.100, D.102, D.105 Ligands: DLY-DPP-DTY.2, DLY-DPP-DTY.2, CA.12, CA.13 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.24, D:D.100, D:D.105, C:G.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baeriswyl, S. et al., X-Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB. Helv.Chim.Acta (2019)

Release Date

2019-08-21

Peptides

Fucose-binding lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fucose-binding lectin

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