Research workbench
PRMT5 bound to the pbm peptide from picln
Analyse PRMT5 bound to the pbm peptide from picln in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V0O
- Type
- protein
- Length
- 944 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 5; Methylosome protein 50; Pbm peptide
- EC
- 2.1.1.320
- UniProt
- O14744, Q9BQA1
- Ligands
- SFG, ACE
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein arginine N-methyltransferase 5 (EC 2.1.1.320) | protein | 625 | 30% helix, 27% strand | O14744 |
| B | Methylosome protein 50 | protein | 309 | 1% helix, 50% strand | Q9BQA1 |
| D | Pbm peptide | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
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 | 602 | 0.85 | 0.90 | 66 | empty |
| 2 | 519 | 0.83 | 0.89 | 55 | empty |
| 3 | 377 | 0.79 | 0.88 | 49 | SFG, ACE |
| 4 | 407 | 0.65 | 0.78 | 39 | empty |
| 5 | 156 | 0.52 | 0.79 | 40 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2159 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 547 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6V0O · PRMT5 bound to the PBM peptide from pICln · 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 0.98
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 6V0O · PDBe 6V0O · UniProt O14744 · UniProt Q9BQA1
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