MolNFT v1 · #127578 · protein
Crystal structure of opha-DELTAC6 mutant Y66F in complex with SAM
5N0R · Peptide N-methyltransferase: “Crystal structure of opha-DELTAC6 mutant Y66F in complex with SAM”. X-ray diffraction, 2 ligands (SAM, CL), 3 pockets (best druggability 0.76). MolNFT v1 #127578 on GenesisL1: 3D structure, binding…
- PDB
- 5N0R
- Type
- protein
- Length
- 389 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide N-methyltransferase
- Ligands
- SAM, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide N-methyltransferase | protein | 389 | 38% helix, 14% strand | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.76 | 0.83 | 52 | SAM |
| 2 | 200 | 0.50 | 0.76 | 31 | empty |
| 3 | 81 | 0.41 | 0.78 | 16 | empty |
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 5N0R · Crystal structure of OphA-DeltaC6 mutant Y66F in complex with SAM · 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 5N0R · PDBe 5N0R
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