Research workbench
Crystal structure of mouse CARM1 in complex with inhibitor U2
Analyse Crystal structure of mouse CARM1 in complex with inhibitor U2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K8W
- Type
- protein
- Length
- 1,373 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-arginine methyltransferase CARM1
- EC
- 2.1.1.319
- UniProt
- Q9WVG6
- Ligands
- DXE, GJV
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 344 | 30% helix, 35% strand | Q9WVG6 |
| C | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 343 | 30% helix, 37% strand | Q9WVG6 |
| D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 342 | 30% helix, 36% strand | Q9WVG6 |
Ligands and binding sites
- DXE · 1,2-dimethoxyethane · ligand · 6 copies · chains A, D, C
- GJV · 9-(7-{[amino(iminio)methyl]amino}-5,6,7-trideoxy-beta-D-ribo-heptofuranosyl)-9H-purin-6-amine · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.83 | 0.84 | 125 | GJV, DXE, EDO |
| 2 | 583 | 0.77 | 0.84 | 70 | GJV, EDO |
| 3 | 492 | 0.77 | 0.85 | 58 | GJV, DXE |
| 4 | 218 | 0.62 | 0.82 | 28 | empty |
| 5 | 215 | 0.57 | 0.79 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1899 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1885 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 762 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 178 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 177 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5K8W · Crystal structure of mouse CARM1 in complex with inhibitor U2 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WVG6 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q9WVG6) · a predicted model of the same protein · 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 Q9WVG6
- Elsewhere: RCSB PDB 5K8W · PDBe 5K8W · UniProt Q9WVG6
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