MolNFT v1 · #145936 · protein
Crystal structure of human CARM1 with (S)-ski-72
6D2L · Histone-arginine methyltransferase CARM1: “Crystal structure of human CARM1 with (S)-ski-72”. X-ray diffraction, 3 ligands (FTG, SO4, UNX), 16 pockets (best druggability 0.76). MolNFT v1 #145936 on GenesisL1: 3D structure, binding…
- PDB
- 6D2L
- Type
- protein
- Length
- 1,976 residues
- Chains
- 6
- 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
- FTG, SO4, UNX
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 330 | 28% helix, 37% strand | Q86X55 |
| D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 329 | 28% helix, 37% strand | Q86X55 |
| E | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 329 | 28% helix, 38% strand | Q86X55 |
| F | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 328 | 29% helix, 38% strand | Q86X55 |
Ligands and binding sites
- FTG · (2S,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-hydroxyphenyl) ethyl]hexanamide · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, F
- UNX · Unknown atom or ion · ion · 3 copies · chains A, C, F
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.76 | 0.79 | 90 | FTG |
| 2 | 892 | 0.75 | 0.79 | 71 | empty |
| 3 | 481 | 0.75 | 0.83 | 56 | FTG |
| 4 | 449 | 0.74 | 0.84 | 55 | FTG |
| 5 | 524 | 0.74 | 0.82 | 53 | FTG |
Interfaces
10 interfaces between chains.
- C–D · 1769 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1756 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1740 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 734 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 293 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6D2L · Crystal structure of human CARM1 with (S)-SKI-72 · the same entry in another collection · chain F against F, TM-score 1.00
- Q86X55 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q86X55) · a predicted model of the same protein · chain C 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 6D2L · PDBe 6D2L · UniProt Q86X55
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