MolNFT v1 · #67838 · protein

T. maritima adometdc in processed form

3IWB · S-adenosylmethionine decarboxylase: “T. maritima adometdc in processed form”. X-ray diffraction, 1 ligand (PYR), 2 pockets (best druggability 0.50). MolNFT v1 #67838 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3IWB
Type: protein
Length: 228 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S-adenosylmethionine decarboxylase
EC: 4.1.1.50
UniProt: Q9WZC3
Ligands: PYR
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	S-adenosylmethionine decarboxylase (EC 4.1.1.50)	protein	59	32% helix, 39% strand	Q9WZC3
A, C	S-adenosylmethionine decarboxylase (EC 4.1.1.50)	protein	55	25% helix, 47% strand	Q9WZC3

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	189	0.50	0.77	24	PYR
2	124	0.46	0.78	23	PYR

Interfaces

6 interfaces between chains.

B–A · 2294 Å² buried · 52 hydrogen bonds · protein-protein
D–C · 2259 Å² buried · 47 hydrogen bonds · protein-protein
A–C · 828 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 380 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 371 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3IWB · T. maritima AdoMetDC in processed form · the same entry in another collection · chain B against B, TM-score 1.00
Q9WZC3 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine decarboxylase proenzyme… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9WZC3
Elsewhere: RCSB PDB 3IWB · PDBe 3IWB · UniProt Q9WZC3

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