MolNFT v1 · #127577 · protein

Crystal structure of opha-DELTAC6 in complex with sah

5N0Q · Peptide N-methyltransferase: “Crystal structure of opha-DELTAC6 in complex with sah”. X-ray diffraction, 1 ligand (SAH), 11 pockets (best druggability 0.81). MolNFT v1 #127577 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5N0Q
Type: protein
Length: 752 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide N-methyltransferase
Ligands: SAH
Pockets: 11 · 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	383	40% helix, 14% strand	—
B	Peptide N-methyltransferase	protein	369	40% 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

11 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	167	0.81	0.97	39	SAH
2	156	0.81	0.97	32	SAH
3	1154	0.78	0.80	89	empty
4	485	0.73	0.82	42	empty
5	144	0.64	0.86	27	empty

Interfaces

1 interface between chains.

A–B · 7033 Å² buried · 80 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 modified (methylation, nonstandard).

Compared structures

5N0Q · Crystal structure of OphA-DeltaC6 in complex with SAH · the same entry in another collection · chain B against B, 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 5N0Q · PDBe 5N0Q

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