MolNFT v1 · #122548 · protein
Crystal structure of mouse CARM1 in complex with inhibitor SA0920 (5'- amino-5'-deoxyadenosine)
5ISI · Histone-arginine methyltransferase CARM1: “Crystal structure of mouse CARM1 in complex with inhibitor SA0920 (5'- amino-5'-deoxyadenosine)”. X-ray diffraction, 2 ligands (5N5, DXE), 11 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5ISI
- 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
- 5N5, DXE
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 343 | 29% helix, 36% strand | Q9WVG6 |
| B | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 342 | 30% helix, 36% strand | Q9WVG6 |
Ligands and binding sites
- 5N5 · 5'-amino-5'-deoxyadenosine · ligand · 4 copies · chains A, B, C, D
- DXE · 1,2-dimethoxyethane · ligand · 2 copies · chains A, 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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.80 | 0.97 | 32 | 5N5 |
| 2 | 164 | 0.80 | 0.96 | 34 | 5N5 |
| 3 | 969 | 0.80 | 0.82 | 102 | 5N5, DXE, EDO |
| 4 | 1173 | 0.77 | 0.79 | 106 | DXE, 5N5, EDO |
| 5 | 209 | 0.58 | 0.80 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1997 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1977 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 834 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 194 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 182 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5ISI · Crystal structure of mouse CARM1 in complex with inhibitor SA0920… · 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 5ISI · PDBe 5ISI · UniProt Q9WVG6
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