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The 1.67 Angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - catalytic dimer (Huc2S2L)
Analyse The 1.67 Angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UUR
- Type
- protein
- Length
- 1,670 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.67
- Source
- Mycolicibacterium smegmatis MC2 155
- Molecule
- Hydrogenase-2, large subunit; Hydrogenase-2, small subunit
- EC
- 1.12.99.6
- UniProt
- A0QUM7, I7G634
- Ligands
- F3S, FCO, VK3, 3NI, MG, OH
- Pockets
- 9 · best druggability 0.84
Structure
electron microscopy · resolution 1.67 · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, F | Hydrogenase-2, large subunit (EC 1.12.99.6) | protein | 513 | 45% helix, 18% strand | A0QUM7 |
| D, G | Hydrogenase-2, small subunit (EC 1.12.99.6) | protein | 322 | 33% helix, 16% strand | I7G634 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 6 copies · chains C, D, F, G
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains C, F
- VK3 · Menadione · ligand · 2 copies · chains D, G
- 3NI · Nickel (III) ion · metal · 2 copies · chains C, F
- MG · Magnesium ion · metal · 2 copies · chains C, F
- OH · Hydroxide ion · ion · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.84 | 0.87 | 112 | empty |
| 2 | 66 | 0.73 | 0.98 | 24 | empty |
| 3 | 63 | 0.72 | 0.97 | 23 | empty |
| 4 | 72 | 0.48 | 0.83 | 15 | VK3 |
| 5 | 79 | 0.45 | 0.81 | 15 | VK3 |
Interfaces
5 interfaces between chains.
- F–G · 3272 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 3268 Ų buried · 45 hydrogen bonds · protein-protein
- D–G · 1728 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 807 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 803 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 d-amino (D-amino acid).
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 A0QUM7
- Every structure of UniProt I7G634
- Elsewhere: RCSB PDB 7UUR · PDBe 7UUR · UniProt A0QUM7 · UniProt I7G634
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