MolNFT v1 · #179618 · protein
Co-crystal structure of alpha glucosidase with compound 7
7KB6 · Isoform 2 of neutral alpha-glucosidase ab: “Co-crystal structure of alpha glucosidase with compound 7”. X-ray diffraction, 3 ligands (XOD, CA, SO4), 20 pockets (best druggability 0.68). MolNFT v1 #179618 on GenesisL1: 3D structure…
- PDB
- 7KB6
- Type
- protein
- Length
- 1,872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of neutral alpha-glucosidase ab; Glucosidase 2 subunit beta
- EC
- 3.2.1.207
- UniProt
- O08795
- Ligands
- XOD, CA, SO4
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of neutral alpha-glucosidase ab (EC 3.2.1.207) | protein | 850 | 21% helix, 32% strand | — |
| B, D | Glucosidase 2 subunit beta | protein | 83 | 7% helix, 14% strand | O08795 |
| C | Isoform 2 of neutral alpha-glucosidase ab (EC 3.2.1.207) | protein | 856 | 21% helix, 32% strand | — |
Ligands and binding sites
- XOD · (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(6-{[2-nitro-4-(pyrimidin-2-yl)phenyl]amino}hexyl)amino]cyclohexane-1,2,3,4-tetrol · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 45 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 14 copies · chains A, C, B, D
- PGE · Triethylene glycol · additive · 9 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.68 | 0.82 | 37 | SO4 |
| 2 | 66 | 0.67 | 0.94 | 29 | empty |
| 3 | 76 | 0.62 | 0.91 | 25 | empty |
| 4 | 251 | 0.61 | 0.80 | 38 | EDO, XOD |
| 5 | 282 | 0.60 | 0.78 | 39 | EDO, XOD |
Interfaces
3 interfaces between chains.
- A–C · 872 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 750 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 732 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 covalent (disulfide, additive adduct).
Compared structures
- O08795 · AlphaFold monomer V2.0 prediction for glucosidase 2 subunit beta (O08795) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O08795
- Elsewhere: RCSB PDB 7KB6 · PDBe 7KB6 · UniProt O08795
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