MolNFT v1 · #127575 · protein
Crystal structure of seleno-opha-DELTAC18 in complex with SAM
5N0O · Peptide N-methyltransferase: “Crystal structure of seleno-opha-DELTAC18 in complex with SAM”. X-ray diffraction, 2 ligands (SAM, HSE), 7 pockets (best druggability 0.85). MolNFT v1 #127575 on GenesisL1: 3D structure, binding sites…
- PDB
- 5N0O
- Type
- protein
- Length
- 748 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide N-methyltransferase
- Ligands
- SAM, HSE
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide N-methyltransferase | protein | 376 | 41% helix, 14% strand | — |
| B | Peptide N-methyltransferase | protein | 372 | 40% helix, 14% strand | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- HSE · L-homoserine · ligand · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
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 | 829 | 0.85 | 0.87 | 92 | SAM |
| 2 | 1185 | 0.83 | 0.84 | 86 | SAM, HSE |
| 3 | 408 | 0.62 | 0.77 | 55 | empty |
| 4 | 52 | 0.48 | 0.86 | 14 | empty |
| 5 | 72 | 0.47 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 6006 Ų buried · 72 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered, oxidation).
Compared structures
- 5N0O · Crystal structure of Seleno-OphA-DeltaC18 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 5N0O · PDBe 5N0O
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