Research workbench
Crystal structure of human O-glcnac transferase with udp-glcnac
Analyse Crystal structure of human O-glcnac transferase with udp-glcnac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GZ5
- Type
- protein
- Length
- 2,800 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit
- EC
- 2.4.1.255
- UniProt
- O15294
- Ligands
- UD1, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit (EC 2.4.1.255) | protein | 700 | 51% helix, 13% strand | O15294 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.76 | 0.78 | 95 | UD1 |
| 2 | 415 | 0.74 | 0.84 | 52 | UD1 |
| 3 | 66 | 0.73 | 0.98 | 19 | empty |
| 4 | 63 | 0.72 | 0.98 | 17 | empty |
| 5 | 65 | 0.71 | 0.97 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–C · 767 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 734 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 732 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 601 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 31 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4GZ5 · Crystal structure of human O-GlcNAc Transferase with UDP-GlcNAc · 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
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
- Elsewhere: RCSB PDB 4GZ5 · PDBe 4GZ5 · UniProt O15294
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