Research workbench
Semisynthetic [fefe]-hydrogenase cpi with propane-dithiolato-bridged [2FE] cofactor
Analyse Semisynthetic [fefe]-hydrogenase cpi with propane-dithiolato-bridged [2FE]… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BYR
- Type
- protein
- Length
- 1,143 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, 4WW, MG
- Pockets
- 16 · 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 | 571 | 43% helix, 16% strand | P29166 |
| B | Iron hydrogenase 1 (EC 1.12.7.2) | protein | 572 | 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
- 4WW · bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.80 | 0.99 | 29 | SF4, 4WW |
| 2 | 100 | 0.79 | 0.99 | 29 | SF4, 4WW |
| 3 | 704 | 0.75 | 0.80 | 92 | MG |
| 4 | 273 | 0.66 | 0.83 | 37 | empty |
| 5 | 215 | 0.64 | 0.83 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1601 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5BYR · Semisynthetic [FeFe]-hydrogenase CpI with propane-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 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 5BYR · PDBe 5BYR · UniProt P29166
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