MolNFT v1 · #126387 · protein
Structure of GH36 alpha-galactosidase from thermotoga maritima in a covalent complex with a cyclopropyl carbasugar.
5M1I: “Structure of GH36 alpha-galactosidase from thermotoga maritima in a covalent complex with a cyclopropyl…”. X-ray diffraction, 2 ligands (7D8, SO4), 2 pockets (best druggability 0.70). MolNFT v1 #126387 on GenesisL1: 3D structure…
- PDB
- 5M1I
- Type
- protein
- Length
- 539 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
- 7D8, SO4
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase (EC 3.2.1.22) | protein | 539 | 27% helix, 33% strand | O33835 |
Ligands and binding sites
- 7D8 · (1~{R},2~{S},3~{S},4~{S},6~{R})-4-fluoranyl-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3-diol · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- EDO · 1,2-ethanediol · additive · 12 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 | 491 | 0.70 | 0.80 | 62 | 7D8, EDO |
| 2 | 85 | 0.30 | 0.72 | 23 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5M1I · Structure of GH36 alpha-galactosidase from Thermotoga maritima in a covalent complex 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 O33835
- Elsewhere: RCSB PDB 5M1I · PDBe 5M1I · UniProt O33835
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