Research workbench

YTER/D143N/DGALA-rha

Analyse YTER/D143N/DGALA-rha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GH4
Type: protein
Length: 363 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative glycosyl hydrolase yter
EC: 3.2.1.-
UniProt: O34559
Ligands: GAD, RAM
Pockets: 2 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative glycosyl hydrolase yter (EC 3.2.1.-)	protein	363	57% helix, 7% strand	O34559

Ligands and binding sites

GAD · 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid · ligand · chains A
RAM · alpha-L-rhamnopyranose · sugar · chains A

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	183	0.59	0.82	24	empty
2	60	0.38	0.80	17	RAM, GAD

Compared structures

2GH4 · YteR/D143N/dGalA-Rha · the same entry in another collection · chain A against A, TM-score 1.00
O34559 · AlphaFold monomer V2.0 prediction for unsaturated rhamnogalacturonyl hydrolase yter… · a predicted model of the same protein · 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
Every structure of UniProt O34559
Elsewhere: RCSB PDB 2GH4 · PDBe 2GH4 · UniProt O34559

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