Research workbench
Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.61 A Resolution.
Analyse Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8POW
- Type
- protein
- Length
- 861 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.61
- Source
- Cupriavidus necator H16
- Molecule
- Uptake hydrogenase large subunit; Uptake hydrogenase small subunit
- EC
- 1.12.99.6
- UniProt
- P31891, P31892
- Ligands
- NFV, SF4, F3S, ER2, MG, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.61 · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Uptake hydrogenase large subunit (EC 1.12.99.6) | protein | 597 | 45% helix, 16% strand | P31891 |
| S | Uptake hydrogenase small subunit (EC 1.12.99.6) | protein | 264 | 35% helix, 17% strand | P31892 |
Ligands and binding sites
- NFV · Ni-Fe oxidized active center · ligand · chains L
- SF4 · Iron/sulfur cluster · ligand · chains S
- F3S · FE3-S4 cluster · ligand · chains L, S
- ER2 · Fe4S4 · ligand · chains L, S
- MG · Magnesium ion · metal · chains L
- CL · Chloride ion · ion · 3 copies · chains L, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.78 | 0.97 | 37 | empty |
| 2 | 289 | 0.68 | 0.83 | 27 | CL |
| 3 | 127 | 0.44 | 0.77 | 21 | empty |
| 4 | 53 | 0.34 | 0.78 | 16 | empty |
| 5 | 58 | 0.30 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- L–S · 4012 Ų buried · 70 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- P31891 · AlphaFold monomer V2.0 prediction for uptake hydrogenase large subunit (P31891) · a predicted model of the same protein · chain L against A, TM-score 1.00
- P31892 · AlphaFold monomer V2.0 prediction for uptake hydrogenase small subunit (P31892) · a predicted model of the same protein · chain S 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 P31891
- Every structure of UniProt P31892
- Elsewhere: RCSB PDB 8POW · PDBe 8POW · UniProt P31891 · UniProt P31892
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