MolNFT v1 · #11169 · protein

Human S-adenosylmethionine decarboxylase

1JEN · Protein (S-adenosylmethionine decarboxylase (beta chain)): “Human S-adenosylmethionine decarboxylase”. X-ray diffraction, 1 ligand (PYR), 8 pockets (best druggability 0.59). MolNFT v1 #11169 on GenesisL1: 3D structure, binding sites…

PDB: 1JEN
Type: protein
Length: 606 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (S-adenosylmethionine decarboxylase (beta chain)); Protein (S-adenosylmethionine…
EC: 4.1.1.50
UniProt: P17707
Ligands: PYR
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Protein (S-adenosylmethionine decarboxylase (beta chain)) (EC 4.1.1.50)	protein	57	21% helix, 35% strand	P17707
A	Protein (S-adenosylmethionine decarboxylase (alpha chain)) (EC 4.1.1.50)	protein	248	23% helix, 40% strand	P17707
D	Protein (S-adenosylmethionine decarboxylase (beta chain)) (EC 4.1.1.50)	protein	54	22% helix, 35% strand	P17707
C	Protein (S-adenosylmethionine decarboxylase (alpha chain)) (EC 4.1.1.50)	protein	247	23% helix, 40% strand	P17707

Ligands and binding sites

PYR · Pyruvic acid · ligand · 2 copies · chains B, A, D, C

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	158	0.59	0.83	27	PYR
2	124	0.55	0.83	24	PYR
3	86	0.48	0.83	23	empty
4	191	0.46	0.74	33	empty
5	136	0.43	0.76	20	empty

Interfaces

3 interfaces between chains.

B–A · 3176 Å² buried · 53 hydrogen bonds · protein-protein
D–C · 3036 Å² buried · 47 hydrogen bonds · protein-protein
A–C · 970 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1JEN · Human S-adenosylmethionine decarboxylase · the same entry in another collection · chain C against C, TM-score 1.00
P17707 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine decarboxylase proenzyme… · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P17707
Elsewhere: RCSB PDB 1JEN · PDBe 1JEN · UniProt P17707

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.