Research workbench
Structure of GH36 alpha-galactosidase from thermotoga maritima in complex with intact cyclopropyl-carbasugar.
Analyse Structure of GH36 alpha-galactosidase from thermotoga maritima in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M12
- Type
- protein
- Length
- 534 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase
- EC
- 3.2.1.22
- UniProt
- O33835
- Ligands
- 7D0, MG, SO4
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase (EC 3.2.1.22) | protein | 534 | 27% helix, 32% strand | O33835 |
Ligands and binding sites
- 7D0 · (1~{R},2~{S},3~{S},4~{R},5~{S},6~{S})-5-[3,5-bis(fluoranyl)phenoxy]-1-(hydroxymethyl) bicyclo[4.1.0]heptane-2,3,4-triol · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.69 | 0.80 | 52 | 7D0 |
| 2 | 74 | 0.28 | 0.72 | 20 | empty |
Compared structures
- 5M12 · Structure of GH36 alpha-galactosidase from Thermotoga maritima in complex with intact… · 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 O33835
- Elsewhere: RCSB PDB 5M12 · PDBe 5M12 · UniProt O33835
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