Research workbench
Full length opha V404E in complex with sah
Analyse Full length opha V404E in complex with sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QZZ
- Type
- protein
- Length
- 784 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide N-methyltransferase
- Ligands
- SAH, EME
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide N-methyltransferase | protein | 393 | 41% helix, 14% strand | — |
| B | Peptide N-methyltransferase | protein | 391 | 42% helix, 14% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- EME · N-methyl-L-glutamic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.82 | 0.97 | 30 | EME, SAH |
| 2 | 129 | 0.81 | 0.98 | 25 | SAH |
| 3 | 149 | 0.77 | 0.94 | 41 | empty |
| 4 | 545 | 0.76 | 0.84 | 82 | empty |
| 5 | 219 | 0.64 | 0.83 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 7863 Ų buried · 97 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 2 covalent (methylation, covalent ligand).
Compared structures
- 6QZZ · full length OphA V404E in complex with SAH · 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
- Elsewhere: RCSB PDB 6QZZ · PDBe 6QZZ
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.