MolNFT v1 · #117060 · protein
Crystal structure of CARM1, sinefungin, and H3 peptide (R17)
5DX0 · Histone-arginine methyltransferase CARM1: “Crystal structure of CARM1, sinefungin, and H3 peptide (R17)”. X-ray diffraction, 3 ligands (ACE, SFG, SO4), 11 pockets (best druggability 0.81). MolNFT v1 #117060 on GenesisL1: 3D…
- PDB
- 5DX0
- Type
- protein
- Length
- 1,406 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-arginine methyltransferase CARM1; H3 peptide
- EC
- 2.1.1.-, 2.1.1.125
- UniProt
- Q86X55, P84243
- Ligands
- ACE, SFG, SO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-, 2.1.1.125) | protein | 343 | 31% helix, 36% strand | Q86X55 |
| F, H | H3 peptide | protein | 8 | 0% helix, 0% strand | P84243 |
| G, I | H3 peptide | protein | 9 | 0% helix, 0% strand | P84243 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, F, B, G, C, H, D, I
- SFG · Sinefungin · ligand · 4 copies · chains A, F, B, G, C, H, D, I
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, F, G, C, D, H, I
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.81 | 0.82 | 74 | SO4 |
| 2 | 126 | 0.80 | 0.98 | 33 | SFG |
| 3 | 121 | 0.80 | 0.98 | 32 | SFG |
| 4 | 122 | 0.80 | 0.98 | 33 | SFG |
| 5 | 119 | 0.80 | 0.98 | 32 | SFG |
Interfaces
15 interfaces between chains.
- A–B · 1810 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1784 Ų buried · 25 hydrogen bonds · protein-protein
- D–I · 726 Ų buried · 10 hydrogen bonds · protein-protein
- C–H · 716 Ų buried · 11 hydrogen bonds · protein-protein
- B–G · 711 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5DX0 · Crystal structure of CARM1, sinefungin, and H3 peptide (R17) · the same entry in another collection · chain I against I, TM-score 1.00
- Q86X55 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q86X55) · a predicted model of the same protein · chain B 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
- Every structure of UniProt P84243
- Elsewhere: RCSB PDB 5DX0 · PDBe 5DX0 · UniProt Q86X55 · UniProt P84243
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.