Research workbench
Crystal structure of paenibacillus sp. 598K alpha-1,6- glucosyltransferase
Analyse Crystal structure of paenibacillus sp. 598K alpha-1,6- glucosyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X7O
- 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
- MG, CA, NI, SO4
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 38% 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 | 14% helix, 38% strand | A0A193PKW5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 15 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 · 15 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.88 | 0.89 | 106 | empty |
| 2 | 1053 | 0.87 | 0.88 | 118 | MG |
| 3 | 1108 | 0.81 | 0.82 | 84 | empty |
| 4 | 1041 | 0.80 | 0.81 | 68 | empty |
| 5 | 1146 | 0.78 | 0.80 | 83 | empty |
Interfaces
1 interface between chains.
- A–B · 13370 Ų buried · 225 hydrogen bonds · protein-protein
Compared structures
- 5X7O · Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltransferase · 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 5X7O · PDBe 5X7O · UniProt A0A193PKW5
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