Research workbench
Crystal structure of human O-glcnac transferase bound to a peptide from hcf-1 pro-repeat 2 (11-26)
Analyse Crystal structure of human O-glcnac transferase bound to a peptide from hcf-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N39
- Type
- protein
- Length
- 707 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit; Host…
- EC
- 2.4.1.255
- UniProt
- O15294, P51610
- Ligands
- UDP
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit (EC 2.4.1.255) | protein | 697 | 52% helix, 12% strand | O15294 |
| B | Host cell factor 1 | protein | 10 | 0% helix, 0% strand | P51610 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.81 | 0.84 | 92 | UDP |
| 2 | 76 | 0.74 | 0.97 | 16 | empty |
| 3 | 162 | 0.53 | 0.79 | 22 | empty |
| 4 | 111 | 0.38 | 0.75 | 20 | empty |
| 5 | 79 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 812 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4N39 · Crystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat… · the same entry in another collection · chain A against A, TM-score 1.00
- O15294 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- peptide… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P51610 · AlphaFold monomer V2.0 prediction for host cell factor 1 (P51610) · a predicted model of the same protein · chain B against A, TM-score 0.51
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 O15294
- Every structure of UniProt P51610
- Elsewhere: RCSB PDB 4N39 · PDBe 4N39 · UniProt O15294 · UniProt P51610
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