Research workbench
Crystal structure of mouse CARM1 in complex with sinefungin at 2.0 ångströms resolution
Analyse Crystal structure of mouse CARM1 in complex with sinefungin at 2.0 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IS6
- Type
- protein
- Length
- 1,371 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, SFG
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 343 | 30% helix, 36% strand | Q9WVG6 |
| B | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 344 | 30% helix, 36% strand | Q9WVG6 |
| C | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 342 | 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, B, C, D
- SFG · Sinefungin · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, D, B, C
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.83 | 0.84 | 125 | PG4, SFG, DXE |
| 2 | 1058 | 0.83 | 0.84 | 117 | PG4, SFG, EDO |
| 3 | 236 | 0.59 | 0.80 | 35 | empty |
| 4 | 211 | 0.58 | 0.80 | 28 | empty |
| 5 | 110 | 0.44 | 0.78 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1942 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1903 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 776 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 211 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 189 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5IS6 · Crystal structure of mouse CARM1 in complex with Sinefungin at 2.0 Angstroms resolution · 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 5IS6 · PDBe 5IS6 · UniProt Q9WVG6
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