MolNFT v1 · #28853 · protein
Structure of the oxidized unready form of ni-fe hydrogenase
1YQW · Periplasmic [nife] hydrogenase small subunit: “Structure of the oxidized unready form of ni-fe hydrogenase”. X-ray diffraction, 8 ligands (SF4, F3S, FCO), 16 pockets (best druggability 0.81). MolNFT v1 #28853 on GenesisL1: 3D…
- PDB
- 1YQW
- Type
- protein
- Length
- 2,417 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic [nife] hydrogenase small subunit; Periplasmic [nife] hydrogenase large subunit
- EC
- 1.12.2.1
- UniProt
- P18187, P18188
- Ligands
- SF4, F3S, FCO, BCT, NI, FE2, MG, PER
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic [nife] hydrogenase small subunit (EC 1.12.2.1) | protein | 262 | 37% helix, 17% strand | P18187 |
| Q, S | Periplasmic [nife] hydrogenase large subunit (EC 1.12.2.1) | protein | 544 | 49% helix, 16% strand | P18188 |
| R | Periplasmic [nife] hydrogenase large subunit (EC 1.12.2.1) | protein | 545 | 49% helix, 16% strand | P18188 |
| C | Periplasmic [nife] hydrogenase small subunit (EC 1.12.2.1) | protein | 260 | 37% helix, 17% strand | P18187 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, Q, B, R, C, S
- F3S · FE3-S4 cluster · ligand · 3 copies · chains A, Q, B, R, C, S
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 3 copies · chains Q, R, S
- BCT · Bicarbonate ion · ligand · chains Q
- NI · Nickel (II) ion · metal · 3 copies · chains Q, R, S
- FE2 · Fe (II) ion · metal · 3 copies · chains Q, R, S
- MG · Magnesium ion · metal · 3 copies · chains Q, C, R
- PER · Peroxide ion · ion · 3 copies · chains Q, R, S
- GOL · Glycerol · additive · 17 copies · chains A, Q, C, B, R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.81 | 0.82 | 79 | MG |
| 2 | 112 | 0.79 | 0.97 | 47 | empty |
| 3 | 81 | 0.75 | 0.97 | 32 | empty |
| 4 | 609 | 0.72 | 0.80 | 57 | GOL |
| 5 | 53 | 0.72 | 0.98 | 22 | empty |
Interfaces
8 interfaces between chains.
- B–R · 3613 Ų buried · 56 hydrogen bonds · protein-protein
- A–Q · 3584 Ų buried · 58 hydrogen bonds · protein-protein
- C–S · 3568 Ų buried · 56 hydrogen bonds · protein-protein
- R–C · 514 Ų buried · 5 hydrogen bonds · protein-protein
- Q–C · 458 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1YQW · Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase · the same entry in another collection · chain S against S, TM-score 1.00
- P18188 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase large subunit… · a predicted model of the same protein · chain Q against A, TM-score 1.00
- P18187 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase small subunit… · a predicted model of the same protein · chain C 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 P18187
- Every structure of UniProt P18188
- Elsewhere: RCSB PDB 1YQW · PDBe 1YQW · UniProt P18187 · UniProt P18188
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