MolNFT v1 · #84234 · protein
3D structure of the nifese hydrogenase from D. vulgaris hildenborough in the oxidized as-isolated state at 1.33 ångströms
3ZE9 · Periplasmic [nifese] hydrogenase, small subunit: “3D structure of the nifese hydrogenase from D. vulgaris hildenborough in the oxidized as-isolated state at…”. X-ray diffraction, 6 ligands (SF4, FSX, FCO), 4 pockets (best…
- PDB
- 3ZE9
- 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, FSX, FCO, NI, FE2, CL
- Pockets
- 4 · best druggability 0.79
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 · 2 copies · chains A, B
- FSX · Bis-(mu-2-oxo),[(mu-3--sulfido)-bis(mu-2--sulfido)-tris(cys-S)-tri-iron] (aqua)(glu-o)iron(ii) · ligand · chains A, B
- FCO · Carbonmonoxide-(dicyano) iron · ligand · chains B
- NI · Nickel (II) ion · metal · chains B
- FE2 · Fe (II) ion · metal · chains B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.79 | 0.97 | 37 | empty |
| 2 | 258 | 0.58 | 0.78 | 33 | empty |
| 3 | 89 | 0.46 | 0.81 | 19 | empty |
| 4 | 85 | 0.36 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3333 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 covalent (oxidation, covalent ligand, nonstandard).
Compared structures
- 3ZE9 · 3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the oxidized… · 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 3ZE9 · PDBe 3ZE9 · UniProt Q72AS4 · UniProt Q72AS3
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