MolNFT v1 · #152661 · protein
Crystal structure of arabidopsis thaliana JMJ13 catalytic domain in complex with nog and an H3K27ME3 peptide
6IP4 · Arabidopsis JMJ13: “Crystal structure of arabidopsis thaliana JMJ13 catalytic domain in complex with nog and an H3K27ME3 peptide”. X-ray diffraction, 4 ligands (OGA, ZN, NI), 7 pockets (best druggability 0.82). MolNFT v1 #152661 on…
- 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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