MolNFT v1 · #102101 · protein

Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (apo)

4OBU · Pyridoxal-dependent decarboxylase domain protein: “Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (apo)”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.83). MolNFT v1 #102101 on GenesisL1: 3D…

PDB: 4OBU
Type: protein
Length: 3,696 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal-dependent decarboxylase domain protein
UniProt: A7B1V0
Ligands: PLP
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, A, U, G, H, F, B, C	Pyridoxal-dependent decarboxylase domain protein	protein	462	48% helix, 17% strand	A7B1V0

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains E, H, A, U, G, F, B, C

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	186	0.83	0.98	26	empty
2	178	0.82	0.97	29	empty
3	527	0.67	0.78	61	PLP
4	605	0.67	0.76	48	empty
5	491	0.66	0.77	60	PLP

Interfaces

8 interfaces between chains.

E–H · 6494 Å² buried · 67 hydrogen bonds · protein-protein
B–C · 6466 Å² buried · 65 hydrogen bonds · protein-protein
G–B · 172 Å² buried · 1 hydrogen bond · protein-protein
A–U · 137 Å² buried · 0 hydrogen bonds · protein-protein
H–F · 133 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4OBU · Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (apo) · the same entry in another collection · chain F against F, TM-score 1.00
A7B1V0 · AlphaFold monomer V2.0 prediction for tryptophan decarboxylase (A7B1V0) · a predicted model of the same protein · chain E against A, TM-score 0.97

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 A7B1V0
Elsewhere: RCSB PDB 4OBU · PDBe 4OBU · UniProt A7B1V0

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