MolNFT v1 · #137237 · protein
Electrophilic probes for deciphering substrate recognition by O-glcnac transferase
5VIF · Udp-N-acetylglucosamine--peptide N…: “Electrophilic probes for deciphering substrate recognition by O-glcnac transferase”. X-ray diffraction, 2 ligands (UDP, 9C1), 6 pockets (best druggability 0.80). MolNFT v1 #137237 on GenesisL1…
- PDB
- 5VIF
- Type
- protein
- Length
- 695 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; Ckii
- EC
- 2.4.1.255
- UniProt
- O15294
- Ligands
- UDP, 9C1
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% 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 | 683 | 50% helix, 13% strand | O15294 |
| B | Ckii | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A, B
- 9C1 · 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.80 | 0.81 | 113 | UDP, 9C1 |
| 2 | 230 | 0.55 | 0.78 | 28 | empty |
| 3 | 151 | 0.44 | 0.75 | 23 | empty |
| 4 | 68 | 0.33 | 0.76 | 22 | empty |
| 5 | 67 | 0.31 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 630 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5VIF · 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 0.98
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 5VIF · PDBe 5VIF · UniProt O15294
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