MolNFT v1 · #119505 · protein
Crystal structure of human JMJD2A in complex with D-threo-isocitrate
5FY8 · Lysine-specific demethylase 4A: “Crystal structure of human JMJD2A in complex with D-threo-isocitrate”. X-ray diffraction, 3 ligands (N81, NI, ZN), 7 pockets (best druggability 0.72). MolNFT v1 #119505 on GenesisL1: 3D structure…
- PDB
- 5FY8
- Type
- protein
- Length
- 697 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- N81, NI, ZN
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 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 | 350 | 31% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 347 | 30% helix, 24% strand | O75164 |
Ligands and binding sites
- N81 · 3-carboxy-2,3-dideoxy-D-erythro-pentaric 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
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 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 | 359 | 0.72 | 0.83 | 38 | NI, N81 |
| 2 | 371 | 0.71 | 0.83 | 39 | NI, N81 |
| 3 | 714 | 0.70 | 0.77 | 74 | EDO |
| 4 | 119 | 0.50 | 0.80 | 27 | EDO |
| 5 | 220 | 0.47 | 0.74 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 408 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5FY8 · Crystal structure of human JMJD2A in complex with D-threo-isocitrate · 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 5FY8 · PDBe 5FY8 · UniProt O75164
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