MolNFT v1 · #127582 · protein

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

5N0V · Peptide N-methyltransferase: “Crystal structure of opha-DELTAC6 mutant Y76F in complex with sah”. X-ray diffraction, 1 ligand (SAH), 9 pockets (best druggability 0.81). MolNFT v1 #127582 on GenesisL1: 3D structure, binding sites and…

PDB: 5N0V
Type: protein
Length: 776 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide N-methyltransferase
Ligands: SAH
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide N-methyltransferase	protein	385	38% helix, 16% strand	—
B	Peptide N-methyltransferase	protein	391	37% helix, 15% strand	—

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	153	0.81	0.97	29	SAH
2	163	0.81	0.96	27	SAH
3	181	0.76	0.92	37	empty
4	243	0.74	0.89	47	empty
5	377	0.65	0.79	52	empty

Interfaces

1 interface between chains.

A–B · 7664 Å² buried · 92 hydrogen bonds · protein-protein

Compared structures

5N0V · Crystal structure of OphA-DeltaC6 mutant Y76F in complex with SAH · 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 5N0V · PDBe 5N0V

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