SMTL ID : 6s5p.1

Cfucosylated peptide SBL2 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.46 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-tetramer

Ligands

3 x LYS- ALA- ALA- LYS- ALA- CYS- NH2: SBL2(Non-covalent)

LYS-ALA-ALA-LYS-ALA-CYS-NH2.1: 4 residues within 4Å: Chain D: S.24, N.71, T.99 Ligands: ZDC.14 2 PLIP interactions: 2 interactions with chain D Water bridges: D:S.24, D:S.24 LYS-ALA-ALA-LYS-ALA-CYS-NH2.2: 3 residues within 4Å: Chain A: S.24, T.46 Ligands: ZDC.6 Protein-ligand interaction information (PLIP) not available LYS-ALA-ALA-LYS-ALA-CYS-NH2.3: 2 residues within 4Å: Chain B: S.24 Ligands: ZDC.9 Protein-ligand interaction information (PLIP) not available

8 x CA: CALCIUM ION(Non-covalent)

CA.4: 8 residues within 4Å: Chain A: N.22, S.23, D.102, N.104, D.105 Chain B: G.115 Ligands: CA.5, ZDC.6 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:G.115, A:N.22, A:D.102, A:D.105 CA.5: 10 residues within 4Å: Chain A: E.96, D.97, G.98, D.100, N.101, D.102, Y.103, D.105 Ligands: CA.4, ZDC.6 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.7: 8 residues within 4Å: Chain A: G.115 Chain B: N.22, S.23, D.102, N.104, D.105 Ligands: CA.8, ZDC.9 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: 9 residues within 4Å: Chain B: E.96, D.97, D.100, N.101, D.102, Y.103, D.105 Ligands: CA.7, ZDC.9 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.10: 9 residues within 4Å: Chain C: E.96, D.97, D.100, N.101, D.102, Y.103, D.105 Ligands: CA.11, ZDC.12 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.11: 8 residues within 4Å: Chain C: N.22, S.23, D.102, N.104, D.105 Chain D: G.115 Ligands: CA.10, ZDC.12 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.13: 8 residues within 4Å: Chain C: G.115 Chain D: N.22, S.23, D.102, N.104, D.105 Ligands: ZDC.14, CA.15 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.15: 9 residues within 4Å: Chain D: E.96, D.97, G.98, D.100, D.102, Y.103, D.105 Ligands: CA.13, 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.6: 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 Chain B: G.115 Ligands: LYS.2, CA.4, CA.5 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.46 Hydrogen bonds: A:S.24, A:S.24, A:D.102, A:D.105, B:G.115 ZDC.9: 14 residues within 4Å: Chain A: G.115 Chain B: N.22, S.23, S.24, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Ligands: LYS.3, CA.7, CA.8 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.24, B:S.24, B:D.97, B:D.102, A:G.115 ZDC.12: 13 residues within 4Å: Chain C: N.22, S.23, S.24, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain D: G.115 Ligands: CA.10, CA.11 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.24, C:D.97, C:D.102, D:G.115 ZDC.14: 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 Ligands: LYS-ALA-ALA-LYS-ALA-CYS-NH2.1, LYS-ALA-ALA-LYS-ALA-CYS-NH2.1, CA.13, CA.15 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.24, D:G.25, D:D.102, D:D.105, C:G.115 Water bridges: D:S.23, D:S.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baeriswyl, S. et al., X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes. Acs Chem.Biol. (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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