Research workbench

A structural view on the dissociation of E. COLI tryptophanase

Analyse A structural view on the dissociation of E. COLI tryptophanase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5D8G
Type: protein
Length: 465 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tryptophanase
EC: 4.1.99.1
UniProt: P0A853
Ligands: MG, NA, CA, CL
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tryptophanase (EC 4.1.99.1)	protein	465	46% helix, 14% strand	P0A853

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A
NA · Sodium ion · metal · chains A
CA · Calcium ion · metal · chains A
CL · Chloride ion · ion · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	261	0.62	0.80	26	empty
2	394	0.60	0.76	36	empty
3	330	0.56	0.75	39	EPE
4	196	0.53	0.78	28	empty

Modifications

Observed in the structure: 2 modified (artifact).

Compared structures

5D8G · A structural view on the dissociation of E. coli Tryptophanase · the same entry in another collection · chain A against A, TM-score 1.00
P0A853 · AlphaFold monomer V2.0 prediction for tryptophanase (P0A853) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 P0A853
Elsewhere: RCSB PDB 5D8G · PDBe 5D8G · UniProt P0A853

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