Research workbench
Crystal structure of arabidopsis thaliana JMJ13 catalytic domain in complex with akg
Analyse Crystal structure of arabidopsis thaliana JMJ13 catalytic domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IP0
- Type
- protein
- Length
- 472 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor jumonji (jmj) family protein
- UniProt
- A0A1P8BAS6
- Ligands
- AKG, ZN, NI, SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor jumonji (jmj) family protein | protein | 472 | 40% helix, 19% strand | A0A1P8BAS6 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 13 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.73 | 0.80 | 57 | AKG, NI, SO4 |
| 2 | 150 | 0.54 | 0.80 | 22 | empty |
| 3 | 149 | 0.53 | 0.81 | 21 | empty |
| 4 | 76 | 0.37 | 0.76 | 17 | empty |
Compared structures
- 6IP0 · Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with AKG · the same entry in another collection · 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 A0A1P8BAS6
- Elsewhere: RCSB PDB 6IP0 · PDBe 6IP0 · UniProt A0A1P8BAS6
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