MolNFT v1 · #108303 · protein
JMJD2A complexed with NI(II), nog and histone H3K27ME3 peptide (16-35)
4V2W · Lysine-specific demethylase 4A: “JMJD2A complexed with NI(II), nog and histone H3K27ME3 peptide (16-35)”. X-ray diffraction, 4 ligands (OGA, NI, ZN), 8 pockets (best druggability 0.74). MolNFT v1 #108303 on GenesisL1: 3D structure…
- PDB
- 4V2W
- Type
- protein
- Length
- 705 residues
- Chains
- 3
- 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
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 348 | 30% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 353 | 31% helix, 24% strand | O75164 |
| C | Histone H3.1T | protein | 4 | 0% helix, 25% strand | Q16695 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, C, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.74 | 0.87 | 40 | NI, OGA |
| 2 | 403 | 0.72 | 0.83 | 45 | NI, OGA |
| 3 | 698 | 0.69 | 0.76 | 69 | empty |
| 4 | 111 | 0.53 | 0.82 | 24 | empty |
| 5 | 147 | 0.42 | 0.74 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 393 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 331 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
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 4V2W · PDBe 4V2W · UniProt O75164 · UniProt Q16695
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