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Crystal structure of opha-DELTAC6 mutant Y63F in complex with SAM

Analyse Crystal structure of opha-DELTAC6 mutant Y63F in complex with SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5N0N
Type: protein
Length: 397 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide N-methyltransferase
Ligands: SAH, EDT, MG
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide N-methyltransferase	protein	397	38% helix, 14% strand	—

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains A
EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · chains A
MG · Magnesium ion · metal · 2 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	475	0.75	0.83	46	SAH
2	239	0.51	0.76	31	empty
3	78	0.38	0.77	17	empty

Modifications

Observed in the structure: 3 modified (methylation, oxidation).

Compared structures

5N0N · Crystal structure of OphA-DeltaC6 mutant Y63F 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 5N0N · PDBe 5N0N

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