Research workbench
Structure and function of an oxygen tolerant nife hydrogenase from salmonella
Analyse Structure and function of an oxygen tolerant nife hydrogenase from salmonella in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C3O
- Type
- protein
- Length
- 2,537 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase-1 large subunit; Hydrogenase-1 small subunit
- EC
- 1.12.7.2
- UniProt
- Q8ZPH0, Q8ZPG9
- Ligands
- NFU, SF4, F3S, F4S, MG, CL, SO4
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hydrogenase-1 large subunit (EC 1.12.7.2) | protein | 583 | 43% helix, 19% strand | Q8ZPH0 |
| B | Hydrogenase-1 small subunit (EC 1.12.7.2) | protein | 263 | 35% helix, 18% strand | Q8ZPG9 |
| D | Hydrogenase-1 small subunit (EC 1.12.7.2) | protein | 262 | 36% helix, 18% strand | Q8ZPG9 |
| F | Hydrogenase-1 small subunit (EC 1.12.7.2) | protein | 263 | 35% helix, 18% strand | Q8ZPG9 |
Ligands and binding sites
- NFU · formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) · ligand · 3 copies · chains A, C, E
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains B, D, F
- F3S · FE3-S4 cluster · ligand · 3 copies · chains A, B, C, D, E, F
- F4S · FE4-S3 cluster · ligand · 3 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 3 copies · chains A, C, E
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.85 | 0.86 | 116 | CL |
| 2 | 978 | 0.81 | 0.83 | 92 | SO4 |
| 3 | 61 | 0.73 | 0.98 | 27 | empty |
| 4 | 62 | 0.72 | 0.98 | 29 | empty |
| 5 | 62 | 0.72 | 0.97 | 24 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4090 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 4086 Ų buried · 69 hydrogen bonds · protein-protein
- E–F · 4085 Ų buried · 71 hydrogen bonds · protein-protein
- A–D · 836 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 831 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4C3O · Structure and function of an oxygen tolerant NiFe hydrogenase from Salmonella · the same entry in another collection · chain A 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 Q8ZPH0
- Every structure of UniProt Q8ZPG9
- Elsewhere: RCSB PDB 4C3O · PDBe 4C3O · UniProt Q8ZPH0 · UniProt Q8ZPG9
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