MolNFT v1 · #154108 · protein
The crystal structure of cyclopenin-bound asqj quinary complex
6K0F · IRON/ALPHA-ketoglutarate-dependent dioxygenase asqj: “The crystal structure of cyclopenin-bound asqj quinary complex”. X-ray diffraction, 4 ligands (AKG, CQ9, PEO), 3 pockets (best druggability 0.72). MolNFT v1 #154108 on GenesisL1…
- PDB
- 6K0F
- Type
- protein
- Length
- 288 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IRON/ALPHA-ketoglutarate-dependent dioxygenase asqj
- EC
- 1.14.-.-
- UniProt
- Q5AR53
- Ligands
- AKG, CQ9, PEO, FE
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | IRON/ALPHA-ketoglutarate-dependent dioxygenase asqj (EC 1.14.-.-) | protein | 288 | 25% helix, 21% strand | Q5AR53 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains B
- CQ9 · (3~{R},3'~{S})-4-methyl-3'-phenyl-spiro[1~{H}-1,4-benzodiazepine-3,2'-oxirane]-2,5-dione · ligand · chains B
- PEO · Hydrogen peroxide · ligand · chains B
- FE · Fe (III) ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.72 | 0.82 | 49 | FE, AKG, CQ9, PEO |
| 2 | 151 | 0.52 | 0.80 | 22 | empty |
| 3 | 63 | 0.31 | 0.74 | 14 | empty |
Compared structures
- 6K0F · The crystal structure of cyclopenin-bound AsqJ quinary complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q5AR53 · AlphaFold monomer V2.0 prediction for IRON/ALPHA-ketoglutarate- dependent dioxygenase… · a predicted model of the same protein · chain B 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 Q5AR53
- Elsewhere: RCSB PDB 6K0F · PDBe 6K0F · UniProt Q5AR53
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