MolNFT v1 · #143354 · protein
Complex structure of JMJD5 and symmetric dimethyl-arginine (sdma)
6AX3 · Lysine-specific demethylase 8: “Complex structure of JMJD5 and symmetric dimethyl-arginine (sdma)”. X-ray diffraction, 3 ligands (2MR, AKG, ZN), 1 pocket (best druggability 0.59). MolNFT v1 #143354 on GenesisL1: 3D structure…
- PDB
- 6AX3
- Type
- protein
- Length
- 236 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 8
- EC
- 1.14.11.27
- UniProt
- Q8N371
- Ligands
- 2MR, AKG, ZN
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 8 (EC 1.14.11.27) | protein | 236 | 24% helix, 33% strand | Q8N371 |
Ligands and binding sites
- 2MR · N3, N4-dimethylarginine · ligand · chains A
- AKG · 2-oxoglutaric acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.59 | 0.83 | 31 | 2MR, AKG, ZN |
Compared structures
- 6AX3 · Complex structure of JMJD5 and Symmetric Dimethyl-Arginine (SDMA) · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N371 · AlphaFold monomer V2.0 prediction for bifunctional peptidase and arginyl-hydroxylase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8N371
- Elsewhere: RCSB PDB 6AX3 · PDBe 6AX3 · UniProt Q8N371
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