MolNFT v1 · #6940 · protein
Crystal structure of the oxidized form of ni-fe hydrogenase
1FRV: “Crystal structure of the oxidized form of ni-fe hydrogenase”. X-ray diffraction, 4 ligands (SF4, F3S, FEL), 17 pockets (best druggability 0.81). MolNFT v1 #6940 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1FRV
- Type
- protein
- Length
- 1,584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase
- EC
- 1.12.2.1
- UniProt
- P12943, P12944
- Ligands
- SF4, F3S, FEL, NI
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hydrogenase (EC 1.12.2.1) | protein | 262 | 30% helix, 16% strand | P12943 |
| B, D | Hydrogenase (EC 1.12.2.1) | protein | 530 | 44% helix, 13% strand | P12944 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B, C, D
- FEL · Hydrated Fe · ligand · 2 copies · chains B, D
- NI · Nickel (II) ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.81 | 0.91 | 74 | empty |
| 2 | 136 | 0.79 | 0.96 | 44 | empty |
| 3 | 1131 | 0.79 | 0.80 | 97 | empty |
| 4 | 60 | 0.57 | 0.89 | 19 | empty |
| 5 | 56 | 0.52 | 0.87 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3633 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 3589 Ų buried · 60 hydrogen bonds · protein-protein
- A–D · 392 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 282 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1FRV · Crystal structure of the oxidized form of ni-fe hydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- P12944 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase large subunit… · a predicted model of the same protein · chain B against A, TM-score 1.00
- P12943 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase small subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P12943
- Every structure of UniProt P12944
- Elsewhere: RCSB PDB 1FRV · PDBe 1FRV · UniProt P12943 · UniProt P12944
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.