MolNFT v1 · #135637 · protein
Coactivator-associated arginine methyltransferase 1 with tp-064
5U4X · Histone-arginine methyltransferase CARM1: “Coactivator-associated arginine methyltransferase 1 with tp-064”. X-ray diffraction, 3 ligands (SAH, 7VM, UNX), 9 pockets (best druggability 0.81). MolNFT v1 #135637 on GenesisL1: 3D…
- PDB
- 5U4X
- Type
- protein
- Length
- 1,322 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-arginine methyltransferase CARM1
- EC
- 2.1.1.319
- UniProt
- Q86X55
- Ligands
- SAH, 7VM, UNX
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 331 | 29% helix, 37% strand | Q86X55 |
| B, C | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 330 | 28% helix, 37% strand | Q86X55 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- 7VM · N-methyl-N-[(2-{1-[2-(methylamino)ethyl]piperidin-4-yl}pyridin-4-yl)methyl]-3-phenoxybenzamide · ligand · 4 copies · chains A, B, C, D
- UNX · Unknown atom or ion · ion · 18 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.81 | 0.83 | 103 | SAH, 7VM, UNX |
| 2 | 487 | 0.74 | 0.82 | 51 | SAH, 7VM, UNX |
| 3 | 469 | 0.72 | 0.82 | 53 | SAH, 7VM, UNX |
| 4 | 262 | 0.63 | 0.81 | 29 | empty |
| 5 | 284 | 0.61 | 0.79 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1711 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1696 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 700 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 192 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 187 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5U4X · Coactivator-associated arginine methyltransferase 1 with TP-064 · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 5U4X · PDBe 5U4X · UniProt Q86X55
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