Research workbench
Full length opha V406P in complex with sah
Analyse Full length opha V406P 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
- 6QZY
- Type
- protein
- Length
- 395 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide N-methyltransferase; Asn-gly-phe-pro-TRP-mva-ile-mva-val-gly-pro-ile-gly
- Ligands
- SAH, MG, SCN
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide N-methyltransferase | protein | 382 | 40% helix, 14% strand | — |
| B | Asn-gly-phe-pro-TRP-mva-ile-mva-val-gly-pro-ile-gly | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- SCN · Thiocyanate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.79 | 0.97 | 26 | SAH |
| 2 | 130 | 0.42 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 914 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6QZY · full length OphA V406P in complex with SAH · the same entry in another collection · chain B against B, 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 6QZY · PDBe 6QZY
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