MolNFT v1 · #114168 · protein
2-OXOACID:FERREDOXIN oxidoreductase 1 from sulfolobus tokodai
5B48 · 2-oxoacid--ferredoxin oxidoreductase alpha subunit: “2-OXOACID:FERREDOXIN oxidoreductase 1 from sulfolobus tokodai”. X-ray diffraction, 3 ligands (SF4, TDN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #114168 on GenesisL1…
- PDB
- 5B48
- Type
- protein
- Length
- 1,653 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoacid--ferredoxin oxidoreductase alpha subunit; 2-oxoacid--ferredoxin oxidoreductase…
- EC
- 1.2.7.-
- UniProt
- Q96Y66, Q96Y68
- Ligands
- SF4, TDN, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoacid--ferredoxin oxidoreductase alpha subunit (EC 1.2.7.-) | protein | 576 | 37% helix, 26% strand | Q96Y66 |
| B | 2-oxoacid--ferredoxin oxidoreductase beta subunit (EC 1.2.7.-) | protein | 286 | 37% helix, 17% strand | Q96Y68 |
| C | 2-oxoacid--ferredoxin oxidoreductase alpha subunit (EC 1.2.7.-) | protein | 560 | 37% helix, 24% strand | Q96Y66 |
| D | 2-oxoacid--ferredoxin oxidoreductase beta subunit (EC 1.2.7.-) | protein | 231 | 40% helix, 23% strand | Q96Y68 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A, B
- TDN · 2-[(2E)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-(1-oxidanylpropylidene)-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate · ligand · chains A, B, C
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.83 | 0.92 | 69 | TDN, MG |
| 2 | 431 | 0.76 | 0.85 | 53 | empty |
| 3 | 395 | 0.72 | 0.83 | 50 | empty |
| 4 | 449 | 0.71 | 0.81 | 43 | empty |
| 5 | 419 | 0.70 | 0.82 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3242 Ų buried · 63 hydrogen bonds · protein-protein
- B–C · 2822 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 2717 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1240 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 934 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5B48 · 2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai · the same entry in another collection · chain D against D, TM-score 1.00
- Q96Y66 · AlphaFold monomer V2.0 prediction for 2-OXOACID:FERREDOXIN oxidoreductase 1, subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q96Y68 · AlphaFold monomer V2.0 prediction for 2-OXOACID:FERREDOXIN oxidoreductase 1, subunit beta… · a predicted model of the same protein · chain B 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 Q96Y66
- Every structure of UniProt Q96Y68
- Elsewhere: RCSB PDB 5B48 · PDBe 5B48 · UniProt Q96Y66 · UniProt Q96Y68
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