Research workbench
Crystal structure of trypanosoma brucei protein arginine methyltransferase 7 complex with adohcy and histone H4 peptide
Analyse Crystal structure of trypanosoma brucei protein arginine methyltransferase 7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M38
- Type
- protein
- Length
- 674 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 7; Histone H4
- EC
- 2.1.1.-
- UniProt
- Q582G4, P62805
- Ligands
- SAH
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein arginine N-methyltransferase 7 (EC 2.1.1.-) | protein | 334 | 30% helix, 28% strand | Q582G4 |
| E | Histone H4 | protein | 4 | 0% helix, 0% strand | P62805 |
| F | Histone H4 | protein | 2 | 0% helix, 0% strand | P62805 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.63 | 0.81 | 31 | SAH |
| 2 | 285 | 0.63 | 0.80 | 32 | SAH |
| 3 | 243 | 0.54 | 0.76 | 31 | empty |
| 4 | 185 | 0.48 | 0.76 | 24 | empty |
| 5 | 71 | 0.43 | 0.81 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3665 Ų buried · 46 hydrogen bonds · protein-protein
- A–E · 382 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 282 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4M38 · Crystal structure of Trypanosoma brucei protein arginine methyltransferase 7 complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q582G4 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 7 (Q582G4) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain E against A, TM-score 0.70
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 Q582G4
- Every structure of UniProt P62805
- Elsewhere: RCSB PDB 4M38 · PDBe 4M38 · UniProt Q582G4 · UniProt P62805
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