Research workbench
Crystal structure of arabidopsis thaliana JMJ13 catalytic domain in complex with nog and an H3K27ME3 peptide
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
- 6IP4
- Type
- protein
- Length
- 479 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arabidopsis JMJ13; Histone H3.2
- UniProt
- F4KIX0, P59226
- Ligands
- OGA, ZN, NI, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arabidopsis JMJ13 | protein | 471 | 38% helix, 21% strand | F4KIX0 |
| B | Histone H3.2 | protein | 8 | 0% helix, 0% strand | P59226 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.82 | 0.85 | 55 | NI, OGA |
| 2 | 113 | 0.54 | 0.82 | 23 | empty |
| 3 | 138 | 0.47 | 0.78 | 25 | empty |
| 4 | 62 | 0.38 | 0.78 | 14 | empty |
| 5 | 67 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 539 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 6IP4 · Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with NOG and… · the same entry in another collection · chain A against A, TM-score 1.00
- P59226 · AlphaFold monomer V2.0 prediction for histone H3.2 (P59226) · a predicted model of the same protein · chain B against A, TM-score 0.30
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 F4KIX0
- Every structure of UniProt P59226
- Elsewhere: RCSB PDB 6IP4 · PDBe 6IP4 · UniProt F4KIX0 · UniProt P59226
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