MolNFT v1 · #140675 · protein

Pyruvylated beta-D-galactosidase from bacillus sp. HMA207, E163A mutant pyruvylated beta-D-galactose complex

5YIF: “Pyruvylated beta-D-galactosidase from bacillus sp. HMA207, E163A mutant pyruvylated beta-D-galactose complex”. X-ray diffraction, 1 ligand (8VR), 3 pockets (best druggability 0.77). MolNFT v1 #140675 on GenesisL1: 3D structure…

PDB: 5YIF
Type: protein
Length: 918 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvylated beta-D-galactosidase
Ligands: 8VR
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pyruvylated beta-D-galactosidase	protein	459	42% helix, 19% strand	—

Ligands and binding sites

8VR · (2r,4ar,6r,7r,8r,8ar)-2-methyl-6,7,8-tris(oxidanyl)-4, 4A,6,7,8,8A-hexahydropyrano[3,2-d][1,3]dioxine-2-carboxylic acid · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	662	0.77	0.82	51	8VR
2	655	0.77	0.82	51	8VR
3	440	0.67	0.79	43	empty

Interfaces

1 interface between chains.

A–B · 376 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5YIF · Pyruvylated beta-D-galactosidase from Bacillus sp. HMA207, E163A mutant pyruvylated… · 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
Elsewhere: RCSB PDB 5YIF · PDBe 5YIF

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