Research workbench
Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R455)
Analyse Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R455) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DX8
- 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; Methylated PABP1 peptide
- EC
- 2.1.1.-, 2.1.1.125
- UniProt
- Q86X55, P11940
- Ligands
- SFG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-, 2.1.1.125) | protein | 344 | 30% helix, 36% strand | Q86X55 |
| C, D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-, 2.1.1.125) | protein | 343 | 32% helix, 36% strand | Q86X55 |
| E | Methylated PABP1 peptide | protein | 9 | 0% helix, 0% strand | P11940 |
| F | Methylated PABP1 peptide | protein | 9 | 0% helix, 0% strand | P11940 |
| G | Methylated PABP1 peptide | protein | 6 | 0% helix, 0% strand | P11940 |
| H | Methylated PABP1 peptide | protein | 8 | 0% helix, 0% strand | P11940 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 4 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.81 | 0.98 | 32 | SFG |
| 2 | 134 | 0.81 | 0.98 | 33 | SFG |
| 3 | 126 | 0.80 | 0.98 | 31 | SFG |
| 4 | 128 | 0.80 | 0.98 | 32 | SFG |
| 5 | 878 | 0.77 | 0.81 | 76 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1898 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1864 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 783 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 730 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 658 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (nonstandard).
Compared structures
- 5DX8 · Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R455) · the same entry in another collection · chain H against H, 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 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 Q86X55
- Every structure of UniProt P11940
- Elsewhere: RCSB PDB 5DX8 · PDBe 5DX8 · UniProt Q86X55 · UniProt P11940
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.