MolNFT v1 · #114739 · protein
Semisynthetic [fefe]-hydrogenase cpi with sulfur-dithiolato-bridged [2FE] cofactor
5BYS · Iron hydrogenase 1: “Semisynthetic [fefe]-hydrogenase cpi with sulfur-dithiolato-bridged [2FE] cofactor”. X-ray diffraction, 4 ligands (SF4, FES, 4WX), 14 pockets (best druggability 0.80). MolNFT v1 #114739 on GenesisL1: 3D…
- PDB
- 5BYS
- Type
- protein
- Length
- 1,147 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron hydrogenase 1
- EC
- 1.12.7.2
- UniProt
- P29166
- Ligands
- SF4, FES, 4WX, MG
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 576 | 43% helix, 16% strand | P29166 |
| B | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 571 | 43% helix, 16% strand | P29166 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
- 4WX · Bis(cyanido-kappac)(dicarbonyl)-mu-(oxomethylidene)-mu-(sulfanediyldimethanethiolatato-1kappas:2kappas) diiron(2+) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.80 | 0.99 | 27 | SF4, 4WX |
| 2 | 113 | 0.80 | 0.99 | 29 | SF4, 4WX |
| 3 | 976 | 0.79 | 0.81 | 131 | MG |
| 4 | 217 | 0.67 | 0.85 | 34 | empty |
| 5 | 233 | 0.66 | 0.84 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1546 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5BYS · Semisynthetic [FeFe]-hydrogenase CpI with sulfur-dithiolato-bridged [2Fe] cofactor · the same entry in another collection · chain A against A, TM-score 1.00
- P29166 · AlphaFold monomer V2.0 prediction for iron hydrogenase 1 (P29166) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P29166
- Elsewhere: RCSB PDB 5BYS · PDBe 5BYS · UniProt P29166
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