Research workbench
Crystal structure of human CARM1 with (R)-ski-72
Analyse Crystal structure of human CARM1 with (R)-ski-72 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DVR
- Type
- protein
- Length
- 667 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-arginine methyltransferase CARM1
- EC
- 2.1.1.319
- UniProt
- Q86X55
- Ligands
- HDG, P15, UNX
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 337 | 27% helix, 37% strand | Q86X55 |
| B | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 330 | 28% helix, 38% strand | Q86X55 |
Ligands and binding sites
- HDG · (2R,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-[(benzylamino)methyl]-N-[2-(4-methoxyphenyl) ethyl]hexanamide (non-preferred name) · ligand · 2 copies · chains A, B
- P15 · 2,5,8,11,14,17-hexaoxanonadecan-19-ol · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.75 | 0.82 | 53 | HDG, P15 |
| 2 | 537 | 0.75 | 0.82 | 52 | HDG, P15 |
| 3 | 111 | 0.42 | 0.77 | 20 | empty |
| 4 | 54 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1768 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6DVR · Crystal structure of human CARM1 with (R)-SKI-72 · the same entry in another collection · chain A against A, TM-score 1.00
- Q86X55 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q86X55) · a predicted model of the same protein · chain A 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 Q86X55
- Elsewhere: RCSB PDB 6DVR · PDBe 6DVR · UniProt Q86X55
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