MolNFT v1 · #171563 · protein
Structure of [nifese] hydrogenase G491A variant from desulfovibrio vulgaris hildenborough pressurized with oxygen gas - structure G491A- O2
6Z9G · Periplasmic [nifese] hydrogenase, small subunit: “Structure of [nifese] hydrogenase G491A variant from desulfovibrio vulgaris hildenborough pressurized with…”. X-ray diffraction, 7 ligands (SF4, 6ML, FCO), 20 pockets (best…
- PDB
- 6Z9G
- Type
- protein
- Length
- 3,032 residues
- Chains
- 8
- 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, 6ML, FCO, NI, FE2, H2S, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Periplasmic [nifese] hydrogenase, small subunit (EC 1.12.7.2) | protein | 277 | 42% helix, 18% strand | Q72AS4 |
| B, D, F, H | 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 · 12 copies · chains A, B, C, D, E, F, G, H
- 6ML · oxygen-damaged SF4 · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 4 copies · chains B, D, F, H
- NI · Nickel (II) ion · metal · 4 copies · chains B, D, F, H
- FE2 · Fe (II) ion · metal · 4 copies · chains B, D, F, H
- H2S · Hydrosulfuric acid · ion · 4 copies · chains B, D, F, H
- CL · Chloride ion · ion · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.82 | 0.95 | 64 | empty |
| 2 | 149 | 0.80 | 0.96 | 49 | empty |
| 3 | 123 | 0.80 | 0.97 | 42 | empty |
| 4 | 947 | 0.75 | 0.78 | 71 | empty |
| 5 | 87 | 0.74 | 0.96 | 30 | empty |
Interfaces
11 interfaces between chains.
- A–B · 3375 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 3365 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 3350 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 3341 Ų buried · 54 hydrogen bonds · protein-protein
- C–F · 383 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6Z9G · Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough… · 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 6Z9G · PDBe 6Z9G · UniProt Q72AS4 · UniProt Q72AS3
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