MolNFT v1 · #127576 · protein

Crystal structure of opha-DELTAC18 in complex with sah

5N0P · Peptide N-methyltranferase: “Crystal structure of opha-DELTAC18 in complex with sah”. X-ray diffraction, 1 ligand (SAH), 10 pockets (best druggability 0.81). MolNFT v1 #127576 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5N0P
Type: protein
Length: 737 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide N-methyltranferase
Ligands: SAH
Pockets: 10 · 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-methyltranferase	protein	377	40% helix, 15% strand	—
B	Peptide N-methyltranferase	protein	360	41% helix, 16% strand	—

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 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	1085	0.81	0.82	82	SAH
2	384	0.78	0.87	40	SAH, EDO
3	403	0.76	0.85	47	empty
4	360	0.62	0.78	46	empty
5	78	0.51	0.85	29	empty

Interfaces

1 interface between chains.

A–B · 6027 Å² buried · 67 hydrogen bonds · protein-protein

Compared structures

5N0P · Crystal structure of OphA-DeltaC18 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 5N0P · PDBe 5N0P

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