MolNFT v1 · #125697 · protein
Crystal structure of mouse CARM1 in complex with ligand P1C3U
5LGR · Histone-arginine methyltransferase CARM1: “Crystal structure of mouse CARM1 in complex with ligand P1C3U”. X-ray diffraction, 5 ligands (QVR, LPD, ACE), 14 pockets (best druggability 0.82). MolNFT v1 #125697 on GenesisL1: 3D…
- PDB
- 5LGR
- Type
- protein
- Length
- 1,417 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-arginine methyltransferase CARM1; Polyadenylate-binding protein 1
- EC
- 2.1.1.319
- UniProt
- Q9WVG6, P11940
- Ligands
- QVR, LPD, ACE, DXE, SO4
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 344 | 29% helix, 36% strand | Q9WVG6 |
| B, D | Histone-arginine methyltransferase CARM1 (EC 2.1.1.319) | protein | 343 | 30% helix, 36% strand | Q9WVG6 |
| E | Polyadenylate-binding protein 1 | protein | 11 | 0% helix, 9% strand | P11940 |
| F, H | Polyadenylate-binding protein 1 | protein | 12 | 0% helix, 0% strand | P11940 |
| G | Polyadenylate-binding protein 1 | protein | 8 | 0% helix, 0% strand | P11940 |
Ligands and binding sites
- QVR · (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- LPD · L-prolinamide · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- ACE · Acetyl group · ligand · 2 copies · chains E, F, G, H
- DXE · 1,2-dimethoxyethane · ligand · chains A, D
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D, E
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.82 | 0.98 | 35 | QVR |
| 2 | 131 | 0.81 | 0.98 | 35 | QVR |
| 3 | 126 | 0.80 | 0.98 | 31 | QVR |
| 4 | 116 | 0.80 | 0.98 | 32 | QVR |
| 5 | 500 | 0.72 | 0.81 | 45 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1917 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1900 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 866 Ų buried · 16 hydrogen bonds · protein-protein
- D–H · 854 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 795 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- 5LGR · Crystal structure of mouse CARM1 in complex with ligand P1C3u · the same entry in another collection · chain G against G, TM-score 1.00
- Q9WVG6 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q9WVG6) · a predicted model of the same protein · chain A 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 Q9WVG6
- Every structure of UniProt P11940
- Elsewhere: RCSB PDB 5LGR · PDBe 5LGR · UniProt Q9WVG6 · UniProt P11940
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