MolNFT v1 · #183092 · protein
Hydrogenase-2 variant R479K - anaerobically oxidised form
7NEM · Hydrogenase-2 small chain: “Hydrogenase-2 variant R479K - anaerobically oxidised form”. X-ray diffraction, 7 ligands (SF4, F3S, FCO), 14 pockets (best druggability 0.83). MolNFT v1 #183092 on GenesisL1: 3D structure, binding sites…
- PDB
- 7NEM
- Type
- protein
- Length
- 1,638 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase-2 small chain; Hydrogenase-2 large chain
- EC
- 1.12.99.6
- UniProt
- P69741, P0ACE0
- Ligands
- SF4, F3S, FCO, MG, NI, OXY, CL
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S, T | Hydrogenase-2 small chain (EC 1.12.99.6) | protein | 268 | 37% helix, 16% strand | P69741 |
| L, M | Hydrogenase-2 large chain (EC 1.12.99.6) | protein | 551 | 46% helix, 16% strand | P0ACE0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains S, L, T, M
- F3S · FE3-S4 cluster · ligand · 2 copies · chains S, L, T, M
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains L, M
- MG · Magnesium ion · metal · 4 copies · chains L, M
- NI · Nickel (II) ion · metal · 2 copies · chains L, M
- OXY · Oxygen molecule · ion · 2 copies · chains L, M
- CL · Chloride ion · ion · chains T, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.83 | 0.97 | 49 | empty |
| 2 | 734 | 0.79 | 0.83 | 63 | empty |
| 3 | 155 | 0.78 | 0.94 | 43 | OXY |
| 4 | 133 | 0.75 | 0.93 | 27 | empty |
| 5 | 63 | 0.62 | 0.91 | 16 | empty |
Interfaces
6 interfaces between chains.
- T–M · 3799 Ų buried · 61 hydrogen bonds · protein-protein
- S–L · 3780 Ų buried · 56 hydrogen bonds · protein-protein
- S–M · 790 Ų buried · 6 hydrogen bonds · protein-protein
- L–T · 777 Ų buried · 6 hydrogen bonds · protein-protein
- S–T · 751 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7NEM · Hydrogenase-2 variant R479K - anaerobically oxidised form · the same entry in another collection · chain S against S, TM-score 1.00
- P0ACE0 · AlphaFold monomer V2.0 prediction for hydrogenase-2 large chain (P0ACE0) · a predicted model of the same protein · chain L against A, TM-score 1.00
- P69741 · AlphaFold monomer V2.0 prediction for hydrogenase-2 small chain (P69741) · a predicted model of the same protein · chain S 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 P69741
- Every structure of UniProt P0ACE0
- Elsewhere: RCSB PDB 7NEM · PDBe 7NEM · UniProt P69741 · UniProt P0ACE0
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