Research workbench
Crystal structure of PRMT5:MEP50 in complex with mta and H4 peptide
Analyse Crystal structure of PRMT5:MEP50 in complex with mta and H4 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FA5
- Type
- protein
- Length
- 927 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 5; Methylosome protein 50; Histone H4
- EC
- 2.1.1.-, 2.1.1.125
- UniProt
- O14744, Q9BQA1, P62805
- Ligands
- MTA
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 5 (EC 2.1.1.-, 2.1.1.125) | protein | 625 | 32% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 301 | 1% helix, 51% strand | Q9BQA1 |
| C | Histone H4 | protein | 1 | 0% helix, 0% strand | P62805 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.88 | 0.89 | 108 | empty |
| 2 | 113 | 0.78 | 0.97 | 25 | MTA |
| 3 | 344 | 0.56 | 0.75 | 37 | empty |
| 4 | 133 | 0.51 | 0.80 | 24 | empty |
| 5 | 106 | 0.49 | 0.80 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2167 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 249 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5FA5 · Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide · 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 1.00
- 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
- Every structure of UniProt P62805
- Elsewhere: RCSB PDB 5FA5 · PDBe 5FA5 · UniProt O14744 · UniProt Q9BQA1 · UniProt P62805
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