Research workbench
Crystal structure of CARM1, sinefungin, and methylated H3 peptide (R17)
Analyse Crystal structure of CARM1, sinefungin, and methylated H3 peptide (R17) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DWQ
- Type
- protein
- Length
- 1,387 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-arginine methyltransferase CARM1; Methylated H3 peptide
- EC
- 2.1.1.-, 2.1.1.125
- UniProt
- Q86X55, P84243
- Ligands
- SFG, ACE, SO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-, 2.1.1.125) | protein | 342 | 30% helix, 36% strand | Q86X55 |
| B, D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-, 2.1.1.125) | protein | 343 | 29% helix, 37% strand | Q86X55 |
| C | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-, 2.1.1.125) | protein | 342 | 30% helix, 37% strand | Q86X55 |
| F | Methylated H3 peptide | protein | 9 | 0% helix, 0% strand | P84243 |
| G | Methylated H3 peptide | protein | 8 | 0% helix, 0% strand | P84243 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 4 copies · chains A, B, F, C, D, G
- ACE · Acetyl group · ligand · 2 copies · chains B, F, D, G
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, F, C, D, G
- GOL · Glycerol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.83 | 0.84 | 94 | SFG, GOL, SO4 |
| 2 | 984 | 0.83 | 0.84 | 94 | SFG, SO4 |
| 3 | 130 | 0.81 | 0.98 | 32 | SFG |
| 4 | 128 | 0.80 | 0.98 | 31 | SFG |
| 5 | 372 | 0.65 | 0.79 | 39 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1910 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1826 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 742 Ų buried · 10 hydrogen bonds · protein-protein
- D–G · 714 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 692 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 5DWQ · Crystal structure of CARM1, sinefungin, and methylated H3 peptide (R17) · the same entry in another collection · chain C against C, TM-score 1.00
- Q86X55 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q86X55) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain G against A, TM-score 0.45
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 5DWQ · PDBe 5DWQ · UniProt Q86X55 · UniProt P84243
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