Research workbench

Serial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by se-sad using xfel (refined against 13,000 patterns)

Analyse Serial femtosecond X-ray structure of a stem domain of human O-mannose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XFC
Type: protein
Length: 306 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1
EC: 2.4.1.-
UniProt: Q8WZA1
Ligands: MBE
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1 (EC 2.4.1.-)	protein	153	15% helix, 41% strand	Q8WZA1

Ligands and binding sites

MBE · 4-nitrophenyl beta-D-mannopyranoside · ligand · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	239	0.50	0.75	37	empty
2	52	0.37	0.80	14	empty

Interfaces

1 interface between chains.

A–B · 481 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

5XFC · Serial femtosecond X-ray structure of a stem domain of human O-mannose… · the same entry in another collection · chain A against A, TM-score 1.00
Q8WZA1 · AlphaFold monomer V2.0 prediction for protein O-linked-mannose… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q8WZA1
Elsewhere: RCSB PDB 5XFC · PDBe 5XFC · UniProt Q8WZA1

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