Research workbench
Crystal structure of mouse CARM1 in complex with inhibitor SA0271
Analyse Crystal structure of mouse CARM1 in complex with inhibitor SA0271 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IS8
- Type
- protein
- Length
- 1,368 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
- 6D1, SAH
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 353 | 27% helix, 35% strand | Q9WVG6 |
| B | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 332 | 29% helix, 37% strand | Q9WVG6 |
| D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 330 | 28% helix, 37% strand | Q9WVG6 |
Ligands and binding sites
- 6D1 · 5'-{[(3S)-3-amino-3-carboxypropyl](2-chloroethyl)amino}-5'-deoxyadenosine · ligand · 3 copies · chains A, B, C
- SAH · S-adenosyl-L-homocysteine · ligand · chains D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.84 | 0.86 | 115 | 6D1, EDO |
| 2 | 536 | 0.78 | 0.85 | 65 | SAH, EDO |
| 3 | 393 | 0.78 | 0.87 | 49 | 6D1 |
| 4 | 428 | 0.71 | 0.82 | 54 | empty |
| 5 | 157 | 0.44 | 0.75 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1916 Ų buried · 29 hydrogen bonds · protein-protein
- D–C · 1899 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 906 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 195 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 191 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5IS8 · Crystal structure of mouse CARM1 in complex with inhibitor SA0271 · the same entry in another collection · chain C against C, TM-score 1.00
- Q9WVG6 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q9WVG6) · a predicted model of the same protein · chain D 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 Q9WVG6
- Elsewhere: RCSB PDB 5IS8 · PDBe 5IS8 · UniProt Q9WVG6
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