MolNFT v1 · #189563 · protein
The complex structure of beta-1,2-glucosyltransferase from ignavibacterium album with sophorose
7VKY: “The complex structure of beta-1,2-glucosyltransferase from ignavibacterium album with sophorose”. X-ray diffraction, 3 ligands (BGC, GLC, CA), 17 pockets (best druggability 0.74). MolNFT v1 #189563 on GenesisL1: 3D structure…
- PDB
- 7VKY
- Type
- protein
- Length
- 1,407 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,2-glucosyltransferase
- UniProt
- I0AIT9
- Ligands
- BGC, GLC, CA
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-1,2-glucosyltransferase | protein | 706 | 35% helix, 24% strand | I0AIT9 |
| B | Beta-1,2-glucosyltransferase | protein | 701 | 36% helix, 24% strand | I0AIT9 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains B
- CA · Calcium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.74 | 0.88 | 50 | BGC |
| 2 | 102 | 0.73 | 0.95 | 29 | empty |
| 3 | 231 | 0.72 | 0.88 | 43 | GLC, BGC |
| 4 | 376 | 0.70 | 0.82 | 47 | empty |
| 5 | 341 | 0.66 | 0.81 | 55 | CA |
Interfaces
1 interface between chains.
- A–B · 1900 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7VKY · The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with… · 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 I0AIT9
- Elsewhere: RCSB PDB 7VKY · PDBe 7VKY · UniProt I0AIT9
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