Research workbench
O-GlcNAc Transferase in complex with covalent inhibitor
Analyse O-GlcNAc Transferase in complex with covalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E37
- Type
- protein
- Length
- 704 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.531
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- O-GlcNAc transferase subunit p110; Tyr-pro-gly-gly-ser-thr-pro-val-ser-ser-ala-asn
- EC
- 2.4.1.255
- UniProt
- O15294
- Ligands
- HQV
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.531 · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-GlcNAc transferase subunit p110 (EC 2.4.1.255) | protein | 692 | 52% helix, 13% strand | O15294 |
| B | Tyr-pro-gly-gly-ser-thr-pro-val-ser-ser-ala-asn | protein | 12 | 0% helix, 8% strand | — |
Ligands and binding sites
- HQV · (2S,3R,4R,5S,6R)-3-[(2E)-but-2-enoylamino]-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.79 | 0.81 | 117 | HQV |
| 2 | 62 | 0.71 | 0.97 | 17 | empty |
| 3 | 245 | 0.52 | 0.75 | 38 | empty |
| 4 | 142 | 0.39 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 626 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 6E37 · PDBe 6E37 · UniProt O15294
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