MolNFT v1 · #139185 · protein
Crystal structure of paenibacillus sp. 598K alpha-1,6- glucosyltransferase complexed with acarbose
5X7P · Glycoside hydrolase family 31 alpha-glucosidase: “Crystal structure of paenibacillus sp. 598K alpha-1,6- glucosyltransferase complexed with acarbose”. X-ray diffraction, 6 ligands (AC1, GLC, MG), 18 pockets (best druggability 0.86).…
- PDB
- 5X7P
- Type
- protein
- Length
- 2,494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 31 alpha-glucosidase
- EC
- 2.4.1.-, 3.2.1.20
- UniProt
- A0A193PKW5
- Ligands
- AC1, GLC, MG, CA, NI, SO4
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycoside hydrolase family 31 alpha-glucosidase (EC 2.4.1.-, 3.2.1.20) | protein | 1247 | 15% helix, 39% strand | A0A193PKW5 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 9 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 18 copies · chains A, B
- MG · Magnesium ion · metal · 12 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.86 | 0.87 | 132 | MES |
| 2 | 908 | 0.85 | 0.87 | 122 | CA, MES, EDO |
| 3 | 1124 | 0.82 | 0.83 | 86 | MES, EDO |
| 4 | 1092 | 0.81 | 0.83 | 83 | empty |
| 5 | 1094 | 0.78 | 0.80 | 86 | GLC, AC1 |
Interfaces
1 interface between chains.
- A–B · 13389 Ų buried · 227 hydrogen bonds · protein-protein
Compared structures
- 5X7P · Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltransferase complexed 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 A0A193PKW5
- Elsewhere: RCSB PDB 5X7P · PDBe 5X7P · UniProt A0A193PKW5
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