MolNFT v1 · #123666 · protein
E. COLI hydrogenase-1 variant P508A
5JRD · Hydrogenase-1 small chain: “E. COLI hydrogenase-1 variant P508A”. X-ray diffraction, 8 ligands (SF4, F3S, SF3), 15 pockets (best druggability 0.82). MolNFT v1 #123666 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JRD
- Type
- protein
- Length
- 1,690 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase-1 small chain; Hydrogenase-1 large chain
- EC
- 1.12.99.6
- UniProt
- P69740, P0ACD8
- Ligands
- SF4, F3S, SF3, FCO, NI, MG, CL, SO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S, T | Hydrogenase-1 small chain (EC 1.12.99.6) | protein | 264 | 36% helix, 19% strand | P69740 |
| L, M | Hydrogenase-1 large chain (EC 1.12.99.6) | protein | 581 | 44% helix, 16% strand | P0ACD8 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains S, T
- F3S · FE3-S4 cluster · ligand · 2 copies · chains S, L, T, M
- SF3 · FE4-S3 cluster · ligand · 2 copies · chains S, L, T, M
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains L, M
- 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 · 3 copies · chains S, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.82 | 0.85 | 97 | SO4 |
| 2 | 64 | 0.73 | 0.98 | 29 | empty |
| 3 | 52 | 0.72 | 0.99 | 19 | F3S |
| 4 | 51 | 0.72 | 0.99 | 20 | F3S |
| 5 | 54 | 0.69 | 0.97 | 25 | empty |
Interfaces
6 interfaces between chains.
- S–L · 4129 Ų buried · 65 hydrogen bonds · protein-protein
- T–M · 4122 Ų buried · 65 hydrogen bonds · protein-protein
- L–T · 862 Ų buried · 7 hydrogen bonds · protein-protein
- S–M · 852 Ų buried · 7 hydrogen bonds · protein-protein
- S–T · 671 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5JRD · E. coli Hydrogenase-1 variant P508A · the same entry in another collection · chain T against T, 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
- P69740 · AlphaFold monomer V2.0 prediction for hydrogenase-1 small chain (P69740) · 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 P69740
- Every structure of UniProt P0ACD8
- Elsewhere: RCSB PDB 5JRD · PDBe 5JRD · UniProt P69740 · UniProt P0ACD8
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