MolNFT v1 · #139062 · protein

KFLA1895 D451A mutant in complex with isomaltose

5X3K · Glycoside hydrolase family 31: “KFLA1895 D451A mutant in complex with isomaltose”. X-ray diffraction, 2 ligands (GLC, SO4), 12 pockets (best druggability 0.77). MolNFT v1 #139062 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5X3K
Type: protein
Length: 1,417 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycoside hydrolase family 31
UniProt: D2PPM7
Ligands: GLC, SO4
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycoside hydrolase family 31	protein	708	26% helix, 26% strand	D2PPM7
B	Glycoside hydrolase family 31	protein	709	27% helix, 27% strand	D2PPM7

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 10 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	600	0.77	0.83	68	empty
2	621	0.72	0.80	47	empty
3	611	0.71	0.79	51	empty
4	356	0.65	0.79	44	GLC
5	301	0.62	0.79	38	empty

Interfaces

1 interface between chains.

A–B · 777 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5X3K · Kfla1895 D451A mutant in complex with isomaltose · the same entry in another collection · chain A against A, TM-score 1.00
D2PPM7 · AlphaFold monomer V2.0 prediction for 1,3-alpha-isomaltosidase (D2PPM7) · a predicted model of the same protein · 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 D2PPM7
Elsewhere: RCSB PDB 5X3K · PDBe 5X3K · UniProt D2PPM7

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