Research workbench
Crystal structure of CARM1, sinefungin, and PABP1 peptide (R455)
Analyse Crystal structure of CARM1, sinefungin, and 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
- 5DX1
- Type
- protein
- Length
- 1,414 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-arginine methyltransferase CARM1; PABP1 peptide
- EC
- 2.1.1.-, 2.1.1.125
- UniProt
- Q86X55, P11940
- Ligands
- SFG
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 32% 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 | 344 | 31% helix, 36% strand | Q86X55 |
| F | PABP1 peptide | protein | 9 | 0% helix, 0% strand | P11940 |
| G | PABP1 peptide | protein | 10 | 0% helix, 0% strand | P11940 |
| H | PABP1 peptide | protein | 8 | 0% helix, 0% strand | P11940 |
| I | PABP1 peptide | protein | 11 | 0% helix, 0% strand | P11940 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 4 copies · chains A, F, B, G, C, H, D, I
- GOL · Glycerol · additive · 4 copies · chains A, B, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.81 | 0.83 | 96 | empty |
| 2 | 139 | 0.81 | 0.98 | 34 | SFG |
| 3 | 135 | 0.81 | 0.98 | 33 | SFG |
| 4 | 124 | 0.80 | 0.98 | 32 | SFG |
| 5 | 129 | 0.80 | 0.98 | 34 | SFG |
Interfaces
14 interfaces between chains.
- A–B · 1890 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1864 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 759 Ų buried · 7 hydrogen bonds · protein-protein
- B–G · 693 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 679 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 5DX1 · Crystal structure of CARM1, sinefungin, and PABP1 peptide (R455) · 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 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 5DX1 · PDBe 5DX1 · UniProt Q86X55 · UniProt P11940
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