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Structure of [nifese] hydrogenase G491A variant from desulfovibrio vulgaris hildenborough pressurized with krypton gas - structure G491A-kr
Analyse Structure of [nifese] hydrogenase G491A variant from desulfovibrio vulgaris… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z8O
- Type
- protein
- Length
- 1,517 residues
- Chains
- 4
- 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, KR, H2S, CL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic [nifese] hydrogenase, small subunit (EC 1.12.7.2) | protein | 277 | 42% helix, 17% strand | Q72AS4 |
| B, D | Periplasmic [nifese] hydrogenase, large subunit, selenocysteine-containing (EC 1.12.7.2) | protein | 481 | 44% helix, 19% strand | Q72AS3 |
| C | Periplasmic [nifese] hydrogenase, small subunit (EC 1.12.7.2) | protein | 278 | 42% helix, 17% strand | Q72AS4 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, D
- 6ML · oxygen-damaged SF4 · ligand · 2 copies · chains A, B, C, D
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains B, D
- NI · Nickel (II) ion · metal · 2 copies · chains B, D
- FE2 · Fe (II) ion · metal · 2 copies · chains B, D
- KR · Krypton · ion · 20 copies · chains A, B, C, D
- H2S · Hydrosulfuric acid · ion · 2 copies · chains B, D
- CL · Chloride ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.83 | 0.94 | 69 | KR |
| 2 | 267 | 0.82 | 0.93 | 67 | KR |
| 3 | 1193 | 0.80 | 0.81 | 105 | KR |
| 4 | 287 | 0.58 | 0.77 | 32 | empty |
| 5 | 258 | 0.58 | 0.78 | 34 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3339 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 3291 Ų buried · 63 hydrogen bonds · protein-protein
- B–C · 490 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6Z8O · 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 6Z8O · PDBe 6Z8O · UniProt Q72AS4 · UniProt Q72AS3
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