SMTL ID : 6s5s.1

Cfucosylated second generation peptide dendrimer SBD8 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.43 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x PRO- LEU- DPP- PHE- LYS- DPP: SBD8 chain B(Non-functional Binders)

PRO-LEU-DPP-PHE-LYS-DPP.1: 8 residues within 4Å: Ligands: LYS-PRO-LEU.2, LYS-PRO-LEU-DPP-PHE-LYS.3, LYS-PRO-LEU-DPP-PHE-LYS.3, LYS-PRO-LEU-DPP-PHE-LYS.3, LYS-PRO-LEU-DPP-PHE-LYS.3, LYS-PRO-LEU.4, LYS-PRO-LEU.4, NH2.7 No protein-ligand interaction detected (PLIP)

2 x LYS- PRO- LEU: SBD8 chain C(Non-functional Binders)

LYS-PRO-LEU.2: 8 residues within 4Å: Chain A: S.24 Ligands: PRO-LEU-DPP-PHE-LYS-DPP.1, PRO-LEU-DPP-PHE-LYS-DPP.1, PRO-LEU-DPP-PHE-LYS-DPP.1, LYS-PRO-LEU.4, LYS-PRO-LEU.4, LYS-PRO-LEU.4, ZDC.8 No protein-ligand interaction detected (PLIP) LYS-PRO-LEU.4: 10 residues within 4Å: Chain A: T.99 Ligands: PRO-LEU-DPP-PHE-LYS-DPP.1, PRO-LEU-DPP-PHE-LYS-DPP.1, PRO-LEU-DPP-PHE-LYS-DPP.1, PRO-LEU-DPP-PHE-LYS-DPP.1, LYS-PRO-LEU.2, LYS-PRO-LEU.2, LYS-PRO-LEU-DPP-PHE-LYS.3, LYS-PRO-LEU-DPP-PHE-LYS.3, LYS-PRO-LEU-DPP-PHE-LYS.3 No protein-ligand interaction detected (PLIP)

1 x LYS- PRO- LEU- DPP- PHE- LYS: SBD8 chain D(Non-functional Binders)

LYS-PRO-LEU-DPP-PHE-LYS.3: 6 residues within 4Å: Ligands: PRO-LEU-DPP-PHE-LYS-DPP.1, PRO-LEU-DPP-PHE-LYS-DPP.1, PRO-LEU-DPP-PHE-LYS-DPP.1, PRO-LEU-DPP-PHE-LYS-DPP.1, LYS-PRO-LEU.4, LYS-PRO-LEU.4 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 8 residues within 4Å: Chain A: E.96, D.97, D.100, D.102, Y.103, D.105 Ligands: CA.6, ZDC.8 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.6: 7 residues within 4Å: Chain A: N.22, S.23, D.102, N.104, D.105 Ligands: CA.5, ZDC.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.22, A:D.102, A:D.105

1 x NH2: AMINO GROUP(Non-functional Binders)

NH2.7: 2 residues within 4Å: Ligands: PRO-LEU-DPP-PHE-LYS-DPP.1, PRO-LEU-DPP-PHE-LYS-DPP.1 No protein-ligand interaction detected (PLIP)

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

ZDC.8: 14 residues within 4Å: Chain A: N.22, S.23, S.24, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Ligands: LYS-PRO-LEU.2, LYS-PRO-LEU.2, CA.5, CA.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:D.100, A:D.105 Water bridges: A:D.100

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Fucose-binding lectin

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