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Active semisynthetic [fefe]-hydrogenase cpi with aza-diselenato- bridged [2FE] cofactor
Analyse Active semisynthetic [fefe]-hydrogenase cpi with aza-diselenato- bridged [2FE]… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OEF
- 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, 9SQ, FES, MG
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 574 | 41% helix, 17% strand | P29166 |
| B | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 573 | 41% helix, 17% strand | P29166 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B
- 9SQ · dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethaneselenato- 1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) · ligand · 2 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.81 | 0.99 | 30 | 9SQ, SF4 |
| 2 | 112 | 0.80 | 0.99 | 31 | 9SQ, SF4 |
| 3 | 867 | 0.77 | 0.80 | 96 | MG |
| 4 | 594 | 0.71 | 0.79 | 65 | empty |
| 5 | 382 | 0.65 | 0.80 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 1470 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5OEF · Active semisynthetic [FeFe]-hydrogenase CpI with aza-diselenato-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 A 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 5OEF · PDBe 5OEF · UniProt P29166
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