MolNFT v1 · #121898 · protein
Bicyclic antimibrocial peptides
5I8X · Fucose-binding lectin: “Bicyclic antimibrocial peptides”. X-ray diffraction, 3 ligands (ZDC, CA, NH2), 2 pockets (best druggability 0.35). MolNFT v1 #121898 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I8X
- Type
- protein
- Length
- 464 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin; Dls-lys-cys-lys-leu-cys-lys-lys-NH2
- UniProt
- A0A069Q9V4
- Ligands
- ZDC, CA, NH2
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 66% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin | protein | 114 | 0% helix, 71% strand | A0A069Q9V4 |
| E | Dls-lys-cys-lys-leu-cys-lys-lys-NH2 | protein | 8 | 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 A, D, B, C, E
- CA · Calcium ion · metal · 8 copies · chains A, D, B, C
- NH2 · Amino group · ion · chains B, E
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 | 117 | 0.35 | 0.73 | 19 | empty |
| 2 | 93 | 0.33 | 0.73 | 18 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1340 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1321 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 520 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 519 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 219 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan, 1 modified (glycation, nonstandard).
Compared structures
- 5I8X · Bicyclic antimibrocial peptides · 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 5I8X · PDBe 5I8X · UniProt A0A069Q9V4
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