MolNFT v1 · #166782 · protein
PRMT5 bound to pbm peptide from RIOK1
6V0N · Protein arginine N-methyltransferase 5: “PRMT5 bound to pbm peptide from RIOK1”. X-ray diffraction, 1 ligand (SFG), 6 pockets (best druggability 0.85). MolNFT v1 #166782 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6V0N
- Type
- protein
- Length
- 930 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 5; Methylosome protein 50; RIOK1 pbm peptide
- EC
- 2.1.1.320
- UniProt
- O14744, Q9BQA1
- Ligands
- SFG
- Pockets
- 6 · best druggability 0.85
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 2.1.1.320) | protein | 624 | 33% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 296 | 2% helix, 52% strand | Q9BQA1 |
| C | RIOK1 pbm peptide | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- SFG · Sinefungin · ligand · chains A
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 | 630 | 0.85 | 0.89 | 67 | empty |
| 2 | 526 | 0.83 | 0.89 | 59 | empty |
| 3 | 357 | 0.79 | 0.89 | 48 | SFG |
| 4 | 376 | 0.64 | 0.78 | 41 | empty |
| 5 | 118 | 0.47 | 0.79 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2148 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 509 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6V0N · PRMT5 bound to PBM peptide from Riok1 · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 6V0N · PDBe 6V0N · UniProt O14744 · UniProt Q9BQA1
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