MolNFT v1 · #127580 · protein

Crystal structure of opha-DELTAC6 mutant Y76F in complex with SAM

5N0T · Peptide N-methyltransferase: “Crystal structure of opha-DELTAC6 mutant Y76F in complex with SAM”. X-ray diffraction, 1 ligand (SAM), 10 pockets (best druggability 0.85). MolNFT v1 #127580 on GenesisL1: 3D structure, binding sites…

PDB: 5N0T
Type: protein
Length: 789 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide N-methyltransferase
Ligands: SAM
Pockets: 10 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide N-methyltransferase	protein	395	37% helix, 14% strand	—
B	Peptide N-methyltransferase	protein	394	38% helix, 14% strand	—

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	237	0.85	0.97	34	SAM
2	230	0.84	0.96	35	SAM
3	675	0.80	0.85	99	empty
4	284	0.79	0.91	51	empty
5	374	0.66	0.80	53	empty

Interfaces

1 interface between chains.

A–B · 7622 Å² buried · 89 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

5N0T · Crystal structure of OphA-DeltaC6 mutant Y76F 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 5N0T · PDBe 5N0T

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