MolNFT v1 · #96931 · protein
X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound FE4S4 clusters.
4JYE · Biotin synthetase, putative: “X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound…”. X-ray diffraction, 6 ligands (1N7, SF4, SAH), 2 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 4JYE
- Type
- protein
- Length
- 347 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biotin synthetase, putative
- UniProt
- Q9X0Z6
- Ligands
- 1N7, SF4, SAH, F3S, BR, CO3
- Pockets
- 2 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biotin synthetase, putative | protein | 347 | 42% helix, 14% strand | Q9X0Z6 |
Ligands and binding sites
- 1N7 · Chapso · ligand · 5 copies · chains A
- SF4 · Iron/sulfur cluster · ligand · chains A
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- F3S · FE3-S4 cluster · ligand · chains A
- BR · Bromide ion · ion · 5 copies · chains A
- CO3 · Carbonate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.87 | 0.94 | 65 | SF4, SAH, BR |
| 2 | 60 | 0.33 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4JYE · X-ray snapshots of possible intermediates in the time course of synthesis and degradation… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X0Z6 · AlphaFold monomer V2.0 prediction for [fefe] hydrogenase maturase subunit hyde (Q9X0Z6) · a predicted model of the same protein · 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 Q9X0Z6
- Elsewhere: RCSB PDB 4JYE · PDBe 4JYE · UniProt Q9X0Z6
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