MolNFT v1 · #139187 · protein
Crystal structure of paenibacillus sp. 598K alpha-1,6- glucosyltransferase complexed with isomaltohexaose
5X7R · Glycoside hydrolase family 31 alpha-glucosidase: “Crystal structure of paenibacillus sp. 598K alpha-1,6- glucosyltransferase complexed with isomaltohexaose”. X-ray diffraction, 7 ligands (AC1, GLC, BGC), 20 pockets (best…
- PDB
- 5X7R
- 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, BGC, MG, CA, NI, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 15% 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 | 15% helix, 38% 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 · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 18 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, B
- MG · Magnesium ion · metal · 20 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 16 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 16 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.86 | 0.87 | 113 | empty |
| 2 | 1083 | 0.85 | 0.86 | 125 | MES |
| 3 | 1001 | 0.81 | 0.82 | 66 | MES |
| 4 | 1118 | 0.81 | 0.82 | 85 | MES |
| 5 | 1170 | 0.78 | 0.80 | 80 | BGC, GLC, MES, SO4 |
Interfaces
1 interface between chains.
- A–B · 13325 Ų buried · 223 hydrogen bonds · protein-protein
Compared structures
- 5X7R · 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 5X7R · PDBe 5X7R · UniProt A0A193PKW5
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