MolNFT v1 · #52158 · protein
Structure and topological arrangement of an O-glcnac transferase homolog: insight into molecular control of intracellular glycosylation
2VSN · Xcogt: “Structure and topological arrangement of an O-glcnac transferase homolog: insight into molecular control of…”. X-ray diffraction, 1 ligand (UDP), 7 pockets (best druggability 0.76). MolNFT v1 #52158 on GenesisL1: 3D…
- PDB
- 2VSN
- Type
- protein
- Length
- 1,068 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xcogt
- EC
- 2.4.-.-
- UniProt
- Q4URB5
- Ligands
- UDP
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xcogt (EC 2.4.-.-) | protein | 534 | 51% helix, 11% strand | Q4URB5 |
| B | Xcogt (EC 2.4.-.-) | protein | 534 | 51% helix, 10% strand | Q4URB5 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.76 | 0.80 | 92 | UDP |
| 2 | 469 | 0.71 | 0.81 | 60 | UDP |
| 3 | 474 | 0.61 | 0.75 | 74 | empty |
| 4 | 209 | 0.59 | 0.80 | 40 | empty |
| 5 | 56 | 0.48 | 0.86 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 751 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2VSN · Structure and topological arrangement of an O-GlcNAc transferase homolog: insight into… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q4URB5
- Elsewhere: RCSB PDB 2VSN · PDBe 2VSN · UniProt Q4URB5
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