MolNFT v1 · #127584 · protein
Crystal structure of opha-DELTAC6 in complex with SAM
5N0X · Peptide N-methyltransferase: “Crystal structure of opha-DELTAC6 in complex with SAM”. X-ray diffraction, 2 ligands (SAM, MG), 12 pockets (best druggability 0.81). MolNFT v1 #127584 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5N0X
- Type
- protein
- Length
- 753 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide N-methyltransferase
- Ligands
- SAM, MG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide N-methyltransferase | protein | 374 | 39% helix, 15% strand | — |
| B | Peptide N-methyltransferase | protein | 379 | 40% helix, 15% strand | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.81 | 0.97 | 33 | SAM |
| 2 | 145 | 0.80 | 0.96 | 31 | SAM |
| 3 | 784 | 0.78 | 0.82 | 62 | empty |
| 4 | 629 | 0.76 | 0.83 | 49 | empty |
| 5 | 58 | 0.67 | 0.96 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 7294 Ų buried · 101 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (methylation, nonstandard).
Compared structures
- 5N0X · Crystal structure of OphA-DeltaC6 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 5N0X · PDBe 5N0X
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