MolNFT v1 · #135323 · protein
JMJD2A in complex with NI(II) and alpha-ketoglutarate
5TVR · Lysine-specific demethylase 4A: “JMJD2A in complex with NI(II) and alpha-ketoglutarate”. X-ray diffraction, 3 ligands (AKG, NI, ZN), 8 pockets (best druggability 0.71). MolNFT v1 #135323 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5TVR
- Type
- protein
- Length
- 694 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
- AKG, NI, ZN
- Pockets
- 8 · best druggability 0.71
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 | 348 | 30% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 346 | 29% helix, 25% strand | O75164 |
Ligands and binding sites
- AKG · 2-oxoglutaric 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
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 | 345 | 0.71 | 0.84 | 35 | NI, AKG |
| 2 | 364 | 0.71 | 0.83 | 37 | NI, AKG |
| 3 | 597 | 0.66 | 0.76 | 72 | empty |
| 4 | 133 | 0.52 | 0.81 | 28 | empty |
| 5 | 121 | 0.40 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 474 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5TVR · JMJD2A in complex with Ni(II) and alpha-Ketoglutarate · 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 5TVR · PDBe 5TVR · UniProt O75164
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