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Crystal structure of eukaryotic O-glcnacase hat-like domain

Analyse Crystal structure of eukaryotic O-glcnacase hat-like domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6R45
Type: protein
Length: 409 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-glcnacase
EC: 3.2.1.169
UniProt: A0A0D5X2Y8
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	O-glcnacase (EC 3.2.1.169)	protein	208	44% helix, 26% strand	A0A0D5X2Y8
B	O-glcnacase (EC 3.2.1.169)	protein	201	41% helix, 25% strand	A0A0D5X2Y8

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B

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

Pockets

5 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	66	0.71	0.96	21	empty
2	62	0.50	0.86	20	empty
3	137	0.48	0.78	19	empty
4	156	0.44	0.75	25	empty
5	85	0.37	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 1080 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

6R45 · Crystal structure of eukaryotic O-GlcNAcase HAT-like domain · the same entry in another collection · 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 A0A0D5X2Y8
Elsewhere: RCSB PDB 6R45 · PDBe 6R45 · UniProt A0A0D5X2Y8

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