MolNFT v1 · #180494 · protein
PRMT5-MEP50 complexed with SAM
7L1G · Protein arginine N-methyltransferase 5: “PRMT5-MEP50 complexed with SAM”. X-ray diffraction, 2 ligands (SAM, CL), 8 pockets (best druggability 0.85). MolNFT v1 #180494 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7L1G
- Type
- protein
- Length
- 936 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 5; Methylosome protein 50
- EC
- 2.1.1.320
- UniProt
- O14744, Q9BQA1
- Ligands
- SAM, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 5 (EC 2.1.1.320) | protein | 625 | 31% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 311 | 1% helix, 49% strand | Q9BQA1 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.85 | 0.90 | 65 | EDO |
| 2 | 523 | 0.83 | 0.89 | 56 | CL, EDO |
| 3 | 317 | 0.78 | 0.89 | 46 | SAM |
| 4 | 320 | 0.60 | 0.77 | 39 | CL |
| 5 | 224 | 0.53 | 0.77 | 34 | EDO |
Interfaces
1 interface between chains.
- A–B · 2158 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7L1G · PRMT5-MEP50 Complexed with SAM · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BQA1 · AlphaFold monomer V2.0 prediction for methylosome protein 50 (Q9BQA1) · a predicted model of the same protein · chain B against A, TM-score 0.99
- O14744 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 5 (O14744) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O14744
- Every structure of UniProt Q9BQA1
- Elsewhere: RCSB PDB 7L1G · PDBe 7L1G · UniProt O14744 · UniProt Q9BQA1
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