MolNFT v1 · #156772 · protein
Structure of JMJD6 bound to mono-methyl arginine.
6MEV · Bifunctional arginine demethylase and lysyl-hydroxylase…: “Structure of JMJD6 bound to mono-methyl arginine.”. X-ray diffraction, 3 ligands (AKG, NMM, FE), 20 pockets (best druggability 0.85). MolNFT v1 #156772 on GenesisL1: 3D…
- PDB
- 6MEV
- Type
- protein
- Length
- 2,700 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
- EC
- 1.14.11.-
- UniProt
- Q6NYC1
- Ligands
- AKG, NMM, FE
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-) | protein | 341 | 43% helix, 20% strand | Q6NYC1 |
| B | Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-) | protein | 333 | 39% helix, 20% strand | Q6NYC1 |
| C, G | Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-) | protein | 335 | 43% helix, 21% strand | Q6NYC1 |
| F | Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-) | protein | 334 | 41% helix, 21% strand | Q6NYC1 |
| H | Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-) | protein | 340 | 41% helix, 21% strand | Q6NYC1 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NMM · (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid · ligand · 4 copies · chains A, E, G, H
- FE · Fe (III) 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.85 | 0.86 | 89 | empty |
| 2 | 768 | 0.74 | 0.79 | 49 | empty |
| 3 | 762 | 0.73 | 0.79 | 65 | empty |
| 4 | 556 | 0.72 | 0.80 | 43 | empty |
| 5 | 425 | 0.68 | 0.80 | 54 | AKG |
Interfaces
17 interfaces between chains.
- D–H · 717 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 628 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 513 Ų buried · 9 hydrogen bonds · protein-protein
- E–H · 383 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 314 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 Q6NYC1
- Elsewhere: RCSB PDB 6MEV · PDBe 6MEV · UniProt Q6NYC1
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