MolNFT v1 · #170229 · protein
Fucosylated bicyclic peptide BP71 bound to the fucose binding lectin lecb pa-iil from pseudomonas aeruginosa at 1.7 ångström resolution
6Y0V · Fucose-binding lectin: “Fucosylated bicyclic peptide BP71 bound to the fucose binding lectin lecb pa-iil from pseudomonas aeruginosa…”. X-ray diffraction, 4 ligands (O65, ZDC, CA), 2 pockets (best druggability 0.31). MolNFT v1…
- PDB
- 6Y0V
- Type
- protein
- Length
- 487 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
- 2 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin | protein | 114 | 0% helix, 71% strand | A0A069Q9V4 |
| E | BP71 | protein | 7 | 57% helix, 0% strand | — |
| G, H | BP71 | protein | 12 | 83% helix, 0% strand | — |
Ligands and binding sites
- O65 · 3,5-bis(hydroxymethyl)-4-methyl-benzaldehyde · ligand · 2 copies · chains G, H
- ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 4 copies · chains A, E, C, B, D, G, H
- CA · Calcium ion · metal · 8 copies · chains A, C, B, D
- NH2 · Amino group · ion · 3 copies · chains E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.31 | 0.72 | 19 | empty |
| 2 | 92 | 0.31 | 0.72 | 18 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1346 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1339 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 522 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 214 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 d-amino, 6 covalent, 3 glycan (D-amino acid, covalent ligand, glycation).
Compared structures
- 6Y0V · 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 6Y0V · PDBe 6Y0V · UniProt A0A069Q9V4
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