MolNFT v1 · #126375 · protein

Structure of GH36 alpha-galactosidase from thermotoga maritima in complex with a hydrolysed cyclopropyl carbasugar.

5M16: “Structure of GH36 alpha-galactosidase from thermotoga maritima in complex with a hydrolysed cyclopropyl…”. X-ray diffraction, 3 ligands (7D2, MG, SO4), 3 pockets (best druggability 0.69). MolNFT v1 #126375 on GenesisL1: 3D…

PDB: 5M16
Type: protein
Length: 533 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: 7D2, MG, SO4
Pockets: 3 · 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	533	27% helix, 32% strand	O33835

Ligands and binding sites

7D2 · (1~{R},2~{S},3~{S},4~{S},5~{S},6~{S})-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3,4,5-tetrol · 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

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	455	0.69	0.80	56	7D2
2	64	0.29	0.74	15	empty
3	51	0.25	0.73	17	empty

Compared structures

5M16 · Structure of GH36 alpha-galactosidase from Thermotoga maritima in complex with a… · 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 5M16 · PDBe 5M16 · UniProt O33835

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