Research workbench
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase asqj in complex with 4-methoxycyclopeptin
Analyse FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase asqj in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DAQ
- Type
- protein
- Length
- 288 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytanoyl-CoA dioxygenase family protein (AFU_ORTHOLOGUE AFUA_8G00230)
- UniProt
- Q5AR53
- Ligands
- AKG, 58D, NI
- 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 |
|---|---|---|---|---|---|
| A | Phytanoyl-CoA dioxygenase family protein (AFU_ORTHOLOGUE AFUA_8G00230) | protein | 288 | 25% helix, 21% strand | Q5AR53 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- 58D · (3S)-3-(4-methoxybenzyl)-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
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 | 423 | 0.72 | 0.82 | 49 | NI, AKG, 58D |
| 2 | 159 | 0.53 | 0.80 | 24 | empty |
| 3 | 56 | 0.29 | 0.74 | 14 | empty |
Compared structures
- 5DAQ · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5AR53 · AlphaFold monomer V2.0 prediction for IRON/ALPHA-ketoglutarate- dependent dioxygenase… · a predicted model of the same protein · chain A 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 5DAQ · PDBe 5DAQ · UniProt Q5AR53
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