MolNFT v1 · #127579 · protein

Crystal structure of opha-DELTAC6 mutant Y98A in complex with SAM

5N0S · Peptide N-methyltransferase: “Crystal structure of opha-DELTAC6 mutant Y98A in complex with SAM”. X-ray diffraction, 1 ligand (SAM), 7 pockets (best druggability 0.81). MolNFT v1 #127579 on GenesisL1: 3D structure, binding sites and…

PDB: 5N0S
Type: protein
Length: 805 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide N-methyltransferase
Ligands: SAM
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide N-methyltransferase	protein	401	38% helix, 14% strand	—
B	Peptide N-methyltransferase	protein	404	40% helix, 14% strand	—

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
MLI · Malonate ion · additive · 2 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.81	0.86	74	SAM
2	618	0.81	0.86	65	SAM
3	83	0.71	0.95	23	empty
4	203	0.70	0.87	37	empty
5	422	0.65	0.79	53	empty

Interfaces

1 interface between chains.

A–B · 7792 Å² buried · 101 hydrogen bonds · protein-protein

Compared structures

5N0S · Crystal structure of OphA-DeltaC6 mutant Y98A 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 5N0S · PDBe 5N0S

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