Research workbench
Fucosylated bicyclic peptide BP71 bound to the fucose binding lectin lecb pa-iil from pseudomonas aeruginosa at 1.5 ångström resolution
Analyse Fucosylated bicyclic peptide BP71 bound to the fucose binding lectin lecb… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y0U
- Type
- protein
- Length
- 492 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin; BP71
- UniProt
- A0A069Q9V4
- Ligands
- O65, ZDC, CA, NH2
- Pockets
- 3 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin | protein | 114 | 0% helix, 67% strand | A0A069Q9V4 |
| E, F, H | BP71 | protein | 12 | 75% helix, 0% strand | — |
Ligands and binding sites
- O65 · 3,5-bis(hydroxymethyl)-4-methyl-benzaldehyde · ligand · 3 copies · chains E, F, D, H
- ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 4 copies · chains A, E, B, F, C, D, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- NH2 · Amino group · ion · 3 copies · chains E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.34 | 0.73 | 19 | empty |
| 2 | 98 | 0.33 | 0.73 | 18 | empty |
| 3 | 65 | 0.27 | 0.73 | 20 | ZDC |
Interfaces
9 interfaces between chains.
- A–B · 1334 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1319 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 523 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 522 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 215 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 d-amino, 9 covalent, 3 glycan (D-amino acid, covalent ligand, glycation).
Compared structures
- 6Y0U · Fucosylated Bicyclic peptide bp71 bound to the fucose binding lectin LecB PA-IIL from… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A069Q9V4
- Elsewhere: RCSB PDB 6Y0U · PDBe 6Y0U · UniProt A0A069Q9V4
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