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3D structure of the ni-fe-se hydrogenase from D. vulgaris hildenborough in the as-isolated oxidized state at 1.50 ångströms
Analyse 3D structure of the ni-fe-se 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
- 3ZE6
- Type
- protein
- Length
- 758 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
- SBY, SF4, FSX, FCO, NI, FE2, CL
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic [nifese] hydrogenase, small subunit (EC 1.12.7.2) | protein | 277 | 43% helix, 18% strand | Q72AS4 |
| B | Periplasmic [nifese] hydrogenase, large subunit, selenocys selenocysteine-containing (EC 1.12.7.2) | protein | 481 | 44% helix, 19% strand | Q72AS3 |
Ligands and binding sites
- SBY · 3-[dodecyl(dimethyl)ammonio]propane-1-sulfonate · ligand · 5 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 3 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
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.81 | 0.86 | 78 | SBY |
| 2 | 246 | 0.56 | 0.77 | 30 | empty |
| 3 | 75 | 0.51 | 0.84 | 19 | empty |
| 4 | 64 | 0.34 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3214 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 covalent (oxidation, covalent ligand, nonstandard).
Compared structures
- 3ZE6 · 3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenborough in the… · the same entry in another collection · chain B against B, 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 3ZE6 · PDBe 3ZE6 · UniProt Q72AS4 · UniProt Q72AS3
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