Research workbench
JMJD2A complexed with NI(II), nog and histone H3K27ME3 peptide (25-29) ARK(ME3)SA
Analyse JMJD2A complexed with NI(II), nog and histone H3K27ME3 peptide (25-29)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V2V
- Type
- protein
- Length
- 711 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A; Histone H3.1T
- EC
- 1.14.11.-
- UniProt
- O75164, Q16695
- Ligands
- OGA, NI, ZN, CL
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 353 | 33% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 348 | 30% helix, 25% strand | O75164 |
| C, D | Histone H3.1T | protein | 5 | 0% helix, 20% strand | Q16695 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, C, B, D
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.77 | 0.98 | 25 | OGA, NI |
| 2 | 80 | 0.75 | 0.98 | 23 | OGA, NI |
| 3 | 716 | 0.70 | 0.77 | 76 | empty |
| 4 | 127 | 0.51 | 0.81 | 33 | empty |
| 5 | 118 | 0.50 | 0.80 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 558 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 491 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 376 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 4V2V · JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (25-29) ARK(me3)SA · the same entry in another collection · chain A against A, TM-score 1.00
- Q16695 · AlphaFold monomer V2.0 prediction for histone H3.1T (Q16695) · a predicted model of the same protein · chain C against A, TM-score 0.67
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 O75164
- Every structure of UniProt Q16695
- Elsewhere: RCSB PDB 4V2V · PDBe 4V2V · UniProt O75164 · UniProt Q16695
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