MolNFT v1 · #183101 · protein
Fucosylated heterochiral linear peptide FDLN69 bound to the fucose binding lectin lecb pa-iil from pseudomonas aeruginosa at 2.0 ångström resolution
7NEW · Fucose-binding lectin: “Fucosylated heterochiral linear peptide FDLN69 bound to the fucose binding lectin lecb pa-iil from…”. X-ray diffraction, 3 ligands (ZDC, CA, NH2), 4 pockets (best druggability 0.37). MolNFT v1 #183101 on…
- PDB
- 7NEW
- Type
- protein
- Length
- 481 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin; Heterochiral peptide FDLN69
- UniProt
- A0A069Q9V4
- Ligands
- ZDC, CA, NH2
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin | protein | 114 | 0% helix, 71% strand | A0A069Q9V4 |
| E, G | Heterochiral peptide FDLN69 | protein | 11 | 0% helix, 0% strand | — |
| H | Heterochiral peptide FDLN69 | protein | 2 | 0% helix, 0% strand | — |
| F | Heterochiral peptide FDLN69 | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 4 copies · chains C, D, E, A, B, G, H, F
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- NH2 · Amino group · ion · 2 copies · chains E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.37 | 0.76 | 20 | ZDC |
| 2 | 117 | 0.36 | 0.73 | 18 | empty |
| 3 | 66 | 0.32 | 0.76 | 20 | ZDC, CA |
| 4 | 72 | 0.29 | 0.73 | 17 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1325 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1321 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 518 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 517 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 212 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 d-amino, 4 glycan (D-amino acid, glycosylation).
Compared structures
- 7NEW · Fucosylated heterochiral linear peptide Fdln69 bound to the fucose binding lectin LecB… · 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 7NEW · PDBe 7NEW · UniProt A0A069Q9V4
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