MolNFT v1 · #113080 · protein
Mechanism of hydrogen activation by nife-hydrogenases
5A4M · Hydrogenase-1 large chain: “Mechanism of hydrogen activation by nife-hydrogenases”. X-ray diffraction, 6 ligands (NFV, SF4, F3S), 9 pockets (best druggability 0.83). MolNFT v1 #113080 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5A4M
- Type
- protein
- Length
- 1,687 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase-1 large chain; Hydrogenase-1 small chain
- EC
- 1.12.99.6
- UniProt
- P0ACD8, P69739
- Ligands
- NFV, SF4, F3S, SF3, MG, CL
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Hydrogenase-1 large chain (EC 1.12.99.6) | protein | 581 | 43% helix, 16% strand | P0ACD8 |
| S | Hydrogenase-1 small chain (EC 1.12.99.6) | protein | 263 | 36% helix, 19% strand | P69739 |
| T | Hydrogenase-1 small chain (EC 1.12.99.6) | protein | 262 | 37% helix, 19% strand | P69739 |
Ligands and binding sites
- NFV · Ni-Fe oxidized active center · ligand · 2 copies · chains L, M
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains S, T
- F3S · FE3-S4 cluster · ligand · 2 copies · chains L, S, M, T
- SF3 · FE4-S3 cluster · ligand · 2 copies · chains L, S, M, T
- MG · Magnesium ion · metal · 2 copies · chains L, M
- CL · Chloride ion · ion · 2 copies · chains S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.83 | 0.84 | 101 | empty |
| 2 | 50 | 0.72 | 0.99 | 21 | F3S |
| 3 | 176 | 0.50 | 0.77 | 39 | empty |
| 4 | 139 | 0.46 | 0.77 | 35 | empty |
| 5 | 73 | 0.41 | 0.79 | 13 | empty |
Interfaces
6 interfaces between chains.
- M–T · 4065 Ų buried · 65 hydrogen bonds · protein-protein
- L–S · 4036 Ų buried · 72 hydrogen bonds · protein-protein
- M–S · 866 Ų buried · 7 hydrogen bonds · protein-protein
- L–T · 849 Ų buried · 7 hydrogen bonds · protein-protein
- S–T · 694 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- P0ACD8 · AlphaFold monomer V2.0 prediction for hydrogenase-1 large chain (P0ACD8) · a predicted model of the same protein · chain L against A, TM-score 1.00
- P69739 · AlphaFold monomer V2.0 prediction for hydrogenase-1 small chain (P69739) · a predicted model of the same protein · chain T 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 P0ACD8
- Every structure of UniProt P69739
- Elsewhere: RCSB PDB 5A4M · PDBe 5A4M · UniProt P0ACD8 · UniProt P69739
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