MolNFT v2 · #118851 · protein
Crystal Structure of human JMJD2A complexed with KDOOA011340
5F5I · Lysine-specific demethylase 4A: “Crystal Structure of human JMJD2A complexed with KDOOA011340”. X-ray diffraction at 2.63, 4 ligands (5V1, NI, ZN), 7 pockets (best druggability 0.73). MolNFT v2 #118851 on GenesisL1: 3D structure…
- PDB
- 5F5I
- Type
- protein
- Length
- 689 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.63
- Source
- Homo sapiens
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- 5V1, NI, ZN, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.63 · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 349 | 30% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 340 | 31% helix, 25% strand | O75164 |
Ligands and binding sites
- 5V1 · 2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic acid · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.73 | 0.84 | 43 | NI, 5V1 |
| 2 | 696 | 0.71 | 0.78 | 81 | empty |
| 3 | 360 | 0.71 | 0.83 | 38 | NI, 5V1 |
| 4 | 100 | 0.53 | 0.83 | 22 | empty |
| 5 | 166 | 0.43 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 524 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5F5I · Crystal structure of human JMJD2A complexed with KDOOA011340 · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 5F5I · PDBe 5F5I · UniProt O75164
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