Research workbench
Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R460)
Analyse Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R460) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DXA
- Type
- protein
- Length
- 1,393 residues
- Chains
- 7
- 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
- 10 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 30% 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 | 344 | 30% helix, 36% strand | Q86X55 |
| B, D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-, 2.1.1.125) | protein | 343 | 30% helix, 36% strand | Q86X55 |
| C | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-, 2.1.1.125) | protein | 343 | 30% helix, 36% strand | Q86X55 |
| F, I | Methylated PABP1 peptide | protein | 7 | 0% helix, 0% strand | P11940 |
| G | Methylated PABP1 peptide | protein | 6 | 0% helix, 0% strand | P11940 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 4 copies · chains A, F, B, G, C, D, I
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.81 | 0.98 | 34 | SFG |
| 2 | 129 | 0.81 | 0.98 | 34 | SFG |
| 3 | 130 | 0.80 | 0.98 | 34 | SFG |
| 4 | 1176 | 0.79 | 0.81 | 101 | SFG |
| 5 | 994 | 0.77 | 0.79 | 73 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1895 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1809 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 747 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 637 Ų buried · 15 hydrogen bonds · protein-protein
- D–I · 612 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 5DXA · Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R460) · 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 A against A, TM-score 1.00
- P11940 · AlphaFold monomer V2.0 prediction for polyadenylate-binding protein 1 (P11940) · a predicted model of the same protein · chain G against A, TM-score 0.78
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 5DXA · PDBe 5DXA · UniProt Q86X55 · UniProt P11940
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