Research workbench
JMJD2A/ KDM4A complexed with NI(II), nog and histone H1.4(18-32)K26ME3 peptide (15-mer)
Analyse JMJD2A/ KDM4A complexed with NI(II), nog and histone H1.4(18-32)K26ME3 peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H8P
- Type
- protein
- Length
- 710 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A; Histone H1.4
- EC
- 1.14.11.-
- UniProt
- O75164, P10412
- Ligands
- OGA, NI, ZN, CL
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 346 | 32% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 353 | 33% helix, 24% strand | O75164 |
| C | Histone H1.4 | protein | 6 | 0% helix, 17% strand | P10412 |
| D | Histone H1.4 | protein | 5 | 0% helix, 20% strand | P10412 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, C, B, D
- NI · Nickel (II) ion · metal · 2 copies · chains A, C, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.78 | 0.98 | 26 | NI, OGA |
| 2 | 93 | 0.76 | 0.97 | 24 | NI, OGA |
| 3 | 504 | 0.63 | 0.76 | 49 | empty |
| 4 | 119 | 0.50 | 0.80 | 26 | empty |
| 5 | 107 | 0.49 | 0.81 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 583 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 548 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 520 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6H8P · JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer) · the same entry in another collection · chain A against A, TM-score 1.00
- P10412 · AlphaFold monomer V2.0 prediction for histone H1.4 (P10412) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 P10412
- Elsewhere: RCSB PDB 6H8P · PDBe 6H8P · UniProt O75164 · UniProt P10412
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