Research workbench
The mechanism of hydrogen activation by nife-hydrogenases
Analyse The mechanism of hydrogen activation by nife-hydrogenases in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ADU
- Type
- protein
- Length
- 1,689 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
- FCO, SF4, F3S, SF3, NI, MG, CL, SO4
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Hydrogenase-1 large chain (EC 1.12.99.6) | protein | 581 | 43% helix, 17% 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 | 264 | 36% helix, 18% strand | P69739 |
Ligands and binding sites
- FCO · Carbonmonoxide-(dicyano) iron · 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
- NI · Nickel (II) ion · metal · 2 copies · chains L, M
- MG · Magnesium ion · metal · 2 copies · chains L, M
- CL · Chloride ion · ion · 4 copies · chains S, T
- SO4 · Sulfate ion · ion · 2 copies · chains M, L, S
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.80 | 0.82 | 105 | empty |
| 2 | 53 | 0.72 | 0.99 | 20 | F3S |
| 3 | 68 | 0.72 | 0.97 | 31 | empty |
| 4 | 53 | 0.72 | 0.99 | 20 | F3S |
| 5 | 52 | 0.68 | 0.97 | 25 | empty |
Interfaces
6 interfaces between chains.
- L–S · 4105 Ų buried · 63 hydrogen bonds · protein-protein
- M–T · 4093 Ų buried · 63 hydrogen bonds · protein-protein
- M–S · 845 Ų buried · 7 hydrogen bonds · protein-protein
- L–T · 833 Ų buried · 7 hydrogen bonds · protein-protein
- S–T · 686 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5ADU · The Mechanism of Hydrogen Activation by NiFe-hydrogenases · the same entry in another collection · chain L against L, TM-score 1.00
- 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 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 P0ACD8
- Every structure of UniProt P69739
- Elsewhere: RCSB PDB 5ADU · PDBe 5ADU · UniProt P0ACD8 · UniProt P69739
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