MolNFT v1 · #121888 · protein
Bicyclic antimibrocial peptides
5I8M · Fucose-binding lectin: “Bicyclic antimibrocial peptides”. X-ray diffraction, 3 ligands (ZDC, CA, NH2), 3 pockets (best druggability 0.51). MolNFT v1 #121888 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I8M
- 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-leu-lys-NH2
- UniProt
- A0A069Q9V4
- Ligands
- ZDC, CA, NH2
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 67% 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-leu-lys-NH2 | protein | 8 | 0% helix, 13% 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 A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.51 | 0.76 | 35 | empty |
| 2 | 202 | 0.50 | 0.77 | 35 | empty |
| 3 | 72 | 0.35 | 0.76 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–D · 1365 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1327 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 408 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 237 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 177 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 glycan, 1 modified (glycation, glycosylation, nonstandard).
Compared structures
- 5I8M · 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 5I8M · PDBe 5I8M · UniProt A0A069Q9V4
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