Research workbench
Crystal structure of trypanosoma brucei protein arginine methyltransferase PRMT7 in complex with S-adenosyl-L-homocysteine
Analyse Crystal structure of trypanosoma brucei protein arginine methyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EKU
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine N-methyltransferase, putative
- UniProt
- D6XJ80
- Ligands
- SAH
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine N-methyltransferase, putative | protein | 343 | 29% helix, 28% strand | D6XJ80 |
| B | Arginine N-methyltransferase, putative | protein | 347 | 27% helix, 27% strand | D6XJ80 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.70 | 0.79 | 70 | SAH |
| 2 | 268 | 0.69 | 0.84 | 36 | empty |
| 3 | 336 | 0.65 | 0.80 | 44 | SAH |
| 4 | 71 | 0.48 | 0.83 | 16 | empty |
| 5 | 85 | 0.47 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3947 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5EKU · Crystal Structure of Trypanosoma Brucei Protein Arginine Methyltransferase PRMT7 in… · the same entry in another collection · chain A against A, TM-score 1.00
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 D6XJ80
- Elsewhere: RCSB PDB 5EKU · PDBe 5EKU · UniProt D6XJ80
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