SMTL ID : 6s7g.1

Cfucosylated linker peptide SBL1 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.84 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

4 x LYS- ALA- LYS- ALA- CYS- NH2: SBL1(Non-covalent)

LYS-ALA-LYS-ALA-CYS-NH2.1: 8 residues within 4Å: Chain B: S.23, G.24, V.69, N.70, D.96, G.97, T.98 Ligands: ZDC.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.96 LYS-ALA-LYS-ALA-CYS-NH2.2: 8 residues within 4Å: Chain C: S.22, S.23, G.24, V.69, N.70, D.96, G.97 Ligands: ZDC.13 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.69 Hydrogen bonds: C:S.23, C:S.23, C:N.70, C:D.96 LYS-ALA-LYS-ALA-CYS-NH2.3: 2 residues within 4Å: Chain D: S.23 Ligands: ZDC.15 No protein-ligand interaction detected (PLIP) LYS-ALA-LYS-ALA-CYS-NH2.4: 2 residues within 4Å: Chain A: S.23 Ligands: ZDC.16 Protein-ligand interaction information (PLIP) not available

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 10 residues within 4Å: Chain A: E.95, D.96, G.97, D.99, N.100, D.101, Y.102, D.104 Ligands: CA.6, ZDC.16 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.95, A:D.99, A:D.101, A:D.104, A:D.104 CA.6: 8 residues within 4Å: Chain A: N.21, S.22, D.101, N.103, D.104 Chain C: G.114 Ligands: CA.5, ZDC.16 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:N.21, A:D.101, A:D.104, C:G.114 CA.7: 8 residues within 4Å: Chain A: G.114 Chain C: N.21, S.22, D.101, N.103, D.104 Ligands: CA.12, ZDC.13 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:N.21, C:D.101, C:D.104, A:G.114 CA.8: 9 residues within 4Å: Chain B: E.95, D.96, G.97, D.99, D.101, Y.102, D.104 Ligands: CA.9, 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.9: 8 residues within 4Å: Chain B: N.21, S.22, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.8, ZDC.11 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Metal complexes: D:G.114, B:N.21, B:D.101, B:D.104 CA.10: 8 residues within 4Å: Chain B: G.114 Chain D: N.21, S.22, D.101, N.103, D.104 Ligands: CA.14, ZDC.15 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Metal complexes: D:N.21, D:D.101, D:D.104, B:G.114 CA.12: 10 residues within 4Å: Chain C: E.95, D.96, G.97, D.99, N.100, D.101, Y.102, D.104 Ligands: CA.7, ZDC.13 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.14: 10 residues within 4Å: Chain D: E.95, D.96, G.97, D.99, N.100, D.101, Y.102, D.104 Ligands: CA.10, ZDC.15 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)

ZDC.11: 17 residues within 4Å: Chain B: N.21, S.22, S.23, T.45, E.95, D.96, G.97, D.99, D.101, N.103, D.104 Chain D: G.114 Ligands: LYS-ALA-LYS-ALA-CYS-NH2.1, LYS-ALA-LYS-ALA-CYS-NH2.1, LYS-ALA-LYS-ALA-CYS-NH2.1, CA.8, CA.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.23, B:D.96, B:D.104, D:G.114 ZDC.13: 18 residues within 4Å: Chain A: G.114 Chain C: N.21, S.22, S.23, T.45, E.95, D.96, G.97, D.99, D.101, N.103, D.104 Ligands: LYS-ALA-LYS-ALA-CYS-NH2.2, LYS-ALA-LYS-ALA-CYS-NH2.2, LYS-ALA-LYS-ALA-CYS-NH2.2, LYS-ALA-LYS-ALA-CYS-NH2.2, CA.7, CA.12 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.23, C:D.96, C:G.97, C:D.101, A:G.114 ZDC.15: 15 residues within 4Å: Chain B: G.114 Chain D: N.21, S.22, S.23, T.45, E.95, D.96, G.97, D.99, D.101, D.104 Ligands: LYS-ALA.3, LYS-ALA.3, CA.10, CA.14 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.23, D:D.96, D:D.99, B:G.114 Water bridges: D:S.22 ZDC.16: 15 residues within 4Å: Chain A: N.21, S.22, S.23, T.45, E.95, D.96, G.97, T.98, D.99, D.101, D.104 Chain C: G.114 Ligands: LYS.4, CA.5, CA.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.23, A:D.99, A:D.104 Water bridges: A:E.95

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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