MolNFT v1 · #111706 · protein
Ficin B crystal form II
4YYS · Ficin isoform B: “Ficin B crystal form II”. X-ray diffraction, 1 ligand (PO4), 2 pockets (best druggability 0.36). MolNFT v1 #111706 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YYS
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ficin isoform B
- EC
- 3.4.22.3
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ficin isoform B (EC 3.4.22.3) | protein | 220 | 27% helix, 22% strand | — |
| B | Ficin isoform B (EC 3.4.22.3) | protein | 221 | 27% helix, 24% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A
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 | 74 | 0.36 | 0.77 | 16 | empty |
| 2 | 79 | 0.35 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 514 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, methylation).
Compared structures
- 4YYS · Ficin B crystal form II · 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
- Elsewhere: RCSB PDB 4YYS · PDBe 4YYS
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