Protein profile

VK055_3674

glycogen debranching enzyme GlgX

Genome: KpATCC43816

Gene: glgX AIK82229.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYH9
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Amino acids 658
Annotations 8
Features 25
PDB binders 4
Druggability 0.651

Overview

Basic information about this protein and its source genome.

Accession
VK055_3674
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
glgX AIK82229.1
Status
annotated
Amino acids
658
Structure source
AlphaFold + ColabFold
EC
3.2.1.196
GO
GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0004133 OBSOLETE. Catalysis of the cleavage of branch points in branched glycogen polymers. GO:0005977 The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages. GO:0005980 The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. GO:0004553 Catalysis of the hydrolysis of any O-glycosyl bond. GO:0004135 Catalysis of the hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in glycogen phosphorylase limit dextrin. Limit dextrin is the highly branched core that remains after exhaustive treatment of glycogen with glycogen phosphorylase. It is formed because these enzymes cannot hydrolyze the (1->6) glycosidic linkages present.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
45.122
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.46

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.651
Structure A0A0H3GYH9
Pocket Pocket 8
P2Rank 0.871
Structure A0A0H3GYH9
Pocket Pocket 1
ColabFold model
FPocket 0.604 · Pocket 4
P2Rank 0.922 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 131 / 4744 genomes with a hit
Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0004133 OBSOLETE. Catalysis of the cleavage of branch points in branched glycogen polymers.
  • GO:0005977 The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
  • GO:0005980 The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
  • GO:0004553 Catalysis of the hydrolysis of any O-glycosyl bond.
  • GO:0004135 Catalysis of the hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in glycogen phosphorylase limit dextrin. Limit dextrin is the highly branched core that remains after exhaustive treatment of glycogen with glycogen phosphorylase. It is formed because these enzymes cannot hydrolyze the (1->6) glycosidic linkages present.
  • GO:0120549 Catalysis of the hydrolysis of (1->6)-alpha-D-glucosidic linkages to branches with degrees of polymerization of three or four glucose residues in limit dextrin.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
130 558 SMART SM00642 aamy
130 558 InterPro IPR006047 Glycosyl hydrolase, family 13, catalytic domain
135 565 SUPERFAMILY SSF51445 (Trans)glycosidases
135 565 InterPro IPR017853 Glycoside hydrolase superfamily
571 655 Pfam PF18390 Glycogen debranching enzyme C-terminal domain
571 655 InterPro IPR040784 Glycogen debranching enzyme, C-terminal domain
135 572 Gene3D G3DSA:3.20.20.80 Glycosidases
3 657 Hamap MF_01248 Glycogen debranching enzyme [glgX].
3 657 InterPro IPR022844 Glycogen debranching enzyme, bacterial
11 96 Pfam PF02922 Carbohydrate-binding module 48 (Isoamylase N-terminal domain)
11 96 InterPro IPR004193 Glycoside hydrolase, family 13, N-terminal
185 287 Pfam PF00128 Alpha amylase, catalytic domain
185 287 InterPro IPR006047 Glycosyl hydrolase, family 13, catalytic domain
7 634 NCBIfam TIGR02100 glycogen debranching protein GlgX
7 634 InterPro IPR011837 Glycogen debranching enzyme, GlgX type
1 133 Gene3D G3DSA:2.60.40.10 Immunoglobulins
1 133 InterPro IPR013783 Immunoglobulin-like fold
4 626 PANTHER PTHR43002 GLYCOGEN DEBRANCHING ENZYME
573 657 Gene3D G3DSA:2.60.40.1180 -
573 657 InterPro IPR013780 Glycosyl hydrolase, all-beta
136 561 CDD cd11326 AmyAc_Glg_debranch
11 133 CDD cd02856 E_set_GDE_Isoamylase_N
11 133 InterPro IPR044505 Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain
7 144 SUPERFAMILY SSF81296 E set domains
7 144 InterPro IPR014756 Immunoglobulin E-set

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GYH9
AlphaFold — — full sequence — Viewing
ColabFold VK055_3674
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
8 0.651
7 0.583
4 0.023
5 0.014

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 26.15 0.871
2 8.55 0.389
3 6.24 0.26
4 5.34 0.207
5 3.92 0.125

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

54 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
ARE
3A6O
Q08751 807.7 Da LogP -10.74 TPSA 400.3 3 viol. ✓ Clean C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@…
BTB
3M07
Q8ZPF0 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
FLC
3VGB
Q55088 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
TAM
6JFJ
A0A0C5GWS2 163.2 Da LogP -1.17 TPSA 86.7 ✓ Ro5 ✓ Clean C(CO)C(CCO)(CCO)N

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.