MolNFT v1 · #119234 · protein
Crystal structure of human JMJD2A in complex with compound KDOAM20A
5FPV · Lysine-specific demethylase 4A: “Crystal structure of human JMJD2A in complex with compound KDOAM20A”. X-ray diffraction, 4 ligands (MMK, NI, MN), 20 pockets (best druggability 0.76). MolNFT v1 #119234 on GenesisL1: 3D structure…
- PDB
- 5FPV
- Type
- protein
- Length
- 2,730 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.27, 1.14.11.-
- UniProt
- O75164
- Ligands
- MMK, NI, MN, ZN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.27, 1.14.11.-) | protein | 337 | 30% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.27, 1.14.11.-) | protein | 343 | 30% helix, 25% strand | O75164 |
| C, D, F | Lysine-specific demethylase 4A (EC 1.14.11.27, 1.14.11.-) | protein | 342 | 30% helix, 25% strand | O75164 |
| E | Lysine-specific demethylase 4A (EC 1.14.11.27, 1.14.11.-) | protein | 341 | 30% helix, 25% strand | O75164 |
| G | Lysine-specific demethylase 4A (EC 1.14.11.27, 1.14.11.-) | protein | 343 | 31% helix, 25% strand | O75164 |
| H | Lysine-specific demethylase 4A (EC 1.14.11.27, 1.14.11.-) | protein | 340 | 32% helix, 25% strand | O75164 |
Ligands and binding sites
- MMK · 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NI · Nickel (II) ion · metal · 15 copies · chains A, H, B, C, D, E, G
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.76 | 0.79 | 68 | empty |
| 2 | 775 | 0.74 | 0.79 | 78 | MN, MMK, NI |
| 3 | 813 | 0.74 | 0.79 | 76 | MN, MMK |
| 4 | 1164 | 0.74 | 0.77 | 76 | empty |
| 5 | 814 | 0.74 | 0.78 | 69 | MN, MMK |
Interfaces
11 interfaces between chains.
- A–H · 554 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 540 Ų buried · 2 hydrogen bonds · protein-protein
- C–F · 525 Ų buried · 2 hydrogen bonds · protein-protein
- B–G · 518 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 487 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5FPV · Crystal structure of human JMJD2A in complex with compound KDOAM20A · the same entry in another collection · chain G against G, TM-score 1.00
- O75164 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4A (O75164) · a predicted model of the same protein · chain H 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 5FPV · PDBe 5FPV · UniProt O75164
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