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3D structure of the nifese hydrogenase from D. vulgaris hildenborough in the reduced state at 1.82 ångströms
Analyse 3D structure of the nifese hydrogenase from D. vulgaris hildenborough in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZEA
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic [nifese] hydrogenase, small subunit; Periplasmic [nifese] hydrogenase, large…
- EC
- 1.12.7.2
- UniProt
- Q72AS4, Q72AS3
- Ligands
- SF4, FCO, NI, FE2, H2S
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic [nifese] hydrogenase, small subunit (EC 1.12.7.2) | protein | 279 | 42% helix, 18% strand | Q72AS4 |
| B | Periplasmic [nifese] hydrogenase, large subunit, selenocysteine-containing (EC 1.12.7.2) | protein | 481 | 44% helix, 19% strand | Q72AS3 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B
- FCO · Carbonmonoxide-(dicyano) iron · ligand · chains B
- NI · Nickel (II) ion · metal · chains B
- FE2 · Fe (II) ion · metal · chains B
- H2S · Hydrosulfuric acid · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.72 | 0.97 | 26 | empty |
| 2 | 62 | 0.70 | 0.96 | 23 | empty |
| 3 | 246 | 0.57 | 0.78 | 30 | empty |
| 4 | 72 | 0.42 | 0.80 | 18 | empty |
| 5 | 84 | 0.39 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3332 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard, oxidation).
Compared structures
- 3ZEA · 3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the reduced… · 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 Q72AS4
- Every structure of UniProt Q72AS3
- Elsewhere: RCSB PDB 3ZEA · PDBe 3ZEA · UniProt Q72AS4 · UniProt Q72AS3
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