MolNFT v1 · #92357 · protein
Crystal structure of full length PRMT5/MEP50 complexes from xenopus laevis
4G56 · HSL7 protein: “Crystal structure of full length PRMT5/MEP50 complexes from xenopus laevis”. X-ray diffraction, 1 ligand (SAH), 15 pockets (best druggability 0.87). MolNFT v1 #92357 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4G56
- Type
- protein
- Length
- 1,814 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HSL7 protein; MGC81050 protein
- UniProt
- Q6NUA1, Q6NUD0
- Ligands
- SAH
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HSL7 protein | protein | 617 | 28% helix, 27% strand | Q6NUA1 |
| B | MGC81050 protein | protein | 292 | 2% helix, 47% strand | Q6NUD0 |
| C | HSL7 protein | protein | 602 | 29% helix, 27% strand | Q6NUA1 |
| D | MGC81050 protein | protein | 303 | 3% helix, 49% strand | Q6NUD0 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.87 | 0.90 | 89 | empty |
| 2 | 822 | 0.87 | 0.90 | 70 | empty |
| 3 | 812 | 0.84 | 0.87 | 87 | empty |
| 4 | 515 | 0.81 | 0.87 | 49 | SAH |
| 5 | 386 | 0.80 | 0.89 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2127 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2092 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 1953 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 4G56 · Crystal Structure of full length PRMT5/MEP50 complexes from Xenopus laevis · the same entry in another collection · chain D against D, TM-score 1.00
- Q6NUD0 · AlphaFold monomer V2.0 prediction for methylosome protein 50 (Q6NUD0) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q6NUA1 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 5 (Q6NUA1) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q6NUA1
- Every structure of UniProt Q6NUD0
- Elsewhere: RCSB PDB 4G56 · PDBe 4G56 · UniProt Q6NUA1 · UniProt Q6NUD0
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