MolNFT v1 · #119830 · protein

Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with glcnac- alpha-pnp

5GGL · Protein O-linked-mannose beta-1,2-N…: “Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in…”. X-ray diffraction, 1 ligand (6ZC), 2 pockets (best druggability 0.43). MolNFT v1…

PDB: 5GGL
Type: protein
Length: 305 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: 6ZC
Pockets: 2 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1 (EC 2.4.1.-)	protein	155	15% helix, 41% strand	Q8WZA1
B	Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1 (EC 2.4.1.-)	protein	150	15% helix, 41% strand	Q8WZA1

Ligands and binding sites

6ZC · 4-nitrophenyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside · 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	155	0.43	0.75	22	empty
2	57	0.43	0.83	18	empty

Interfaces

1 interface between chains.

A–B · 457 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5GGL · Crystal structure of N-terminal domain of human protein 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 B 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 5GGL · PDBe 5GGL · UniProt Q8WZA1

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