Research workbench
Electrophilic probes for deciphering substrate recognition by O-glcnac transferase
Analyse Electrophilic probes for deciphering substrate recognition by O-glcnac… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VIE
- Type
- protein
- Length
- 1,357 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; Ckii
- EC
- 2.4.1.255
- UniProt
- O15294
- Ligands
- UDP, 9C1, 9CD
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 50% 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 | 666 | 50% helix, 13% strand | O15294 |
| B, D | Ckii | protein | 12 | 0% helix, 0% strand | — |
| C | Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit (EC 2.4.1.255) | protein | 667 | 51% helix, 12% strand | O15294 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B, C, D
- 9C1 · 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose · ligand · chains A, B
- 9CD · 2-{[(2E)-but-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose · ligand · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.81 | 0.94 | 44 | UDP, 9C1 |
| 2 | 270 | 0.80 | 0.92 | 48 | UDP, 9CD |
| 3 | 972 | 0.78 | 0.80 | 97 | empty |
| 4 | 873 | 0.77 | 0.80 | 87 | empty |
| 5 | 100 | 0.76 | 0.96 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2024 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 635 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 631 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 171 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 168 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 5VIE · Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase · 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 0.99
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 O15294
- Elsewhere: RCSB PDB 5VIE · PDBe 5VIE · UniProt O15294
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