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The 2.19-angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - Complex minus stalk
Analyse The 2.19-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
- 7UTD
- Type
- protein
- Length
- 6,916 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.19
- Source
- Mycolicibacterium smegmatis MC2 155
- Molecule
- Hydrogenase-2, large subunit; Hydrogenase-2, small subunit; Type 2 [NiFe]-hydrogenase Huc…
- EC
- 1.12.99.6
- UniProt
- A0QUM7, I7G634, A0QUM5
- Ligands
- F3S, FCO, MQ9, 3NI, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 2.19 · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | Hydrogenase-2, large subunit (EC 1.12.99.6) | protein | 513 | 45% helix, 18% strand | A0QUM7 |
| B, D, F, H, J, L, N, P | Hydrogenase-2, small subunit (EC 1.12.99.6) | protein | 322 | 32% helix, 16% strand | I7G634 |
| Q, R, S, T | Type 2 [NiFe]-hydrogenase Huc membrane adapter subunit | protein | 59 | 92% helix, 0% strand | A0QUM5 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 8 copies · chains A, C, E, G, I, K, M, O
- MQ9 · Menaquinone-9 · ligand · 8 copies · chains B, Q, D, R, F, H, S, J, T, L, N, P
- 3NI · Nickel (III) ion · metal · 8 copies · chains A, C, E, G, I, K, M, O
- MG · Magnesium ion · metal · 8 copies · chains A, C, E, G, I, K, M, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.84 | 0.87 | 115 | empty |
| 2 | 824 | 0.84 | 0.87 | 103 | empty |
| 3 | 848 | 0.84 | 0.86 | 109 | empty |
| 4 | 833 | 0.84 | 0.87 | 108 | empty |
| 5 | 1175 | 0.81 | 0.81 | 43 | empty |
Interfaces
44 interfaces between chains.
- K–L · 3297 Ų buried · 43 hydrogen bonds · protein-protein
- M–N · 3292 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 3292 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 3290 Ų buried · 44 hydrogen bonds · protein-protein
- O–P · 3287 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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
- Every structure of UniProt A0QUM5
- Elsewhere: RCSB PDB 7UTD · PDBe 7UTD · UniProt A0QUM7 · UniProt I7G634 · UniProt A0QUM5
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