Research workbench
Crystal structure of mouse CARM1 in complex with inhibitor SA0491
Analyse Crystal structure of mouse CARM1 in complex with inhibitor SA0491 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ISC
- Type
- protein
- Length
- 1,370 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
- SAO, 6D0, DXE, M2M
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 342 | 29% helix, 36% strand | Q9WVG6 |
| B | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 342 | 30% helix, 36% strand | Q9WVG6 |
| C, D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 343 | 28% helix, 36% strand | Q9WVG6 |
Ligands and binding sites
- SAO · 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine · ligand · 2 copies · chains A, C
- 6D0 · 5'-{[(3S)-3-amino-3-carboxypropyl](3-bromo-2-oxopropyl)amino}-5'-deoxyadenosine · ligand · 2 copies · chains B, D
- DXE · 1,2-dimethoxyethane · ligand · 2 copies · chains C, D
- M2M · 1-methoxy-2-(2-methoxyethoxy)ethane · ligand · chains C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.87 | 0.87 | 111 | SAO, 6D0 |
| 2 | 592 | 0.81 | 0.86 | 62 | 6D0, EDO |
| 3 | 659 | 0.80 | 0.85 | 67 | SAO, EDO |
| 4 | 300 | 0.63 | 0.80 | 36 | empty |
| 5 | 155 | 0.59 | 0.83 | 17 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1931 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1832 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 791 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 175 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 172 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5ISC · Crystal structure of mouse CARM1 in complex with inhibitor SA0491 · 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 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 5ISC · PDBe 5ISC · UniProt Q9WVG6
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