Protein profile

VK055_0887

beta-galactosidase

Genome: KpATCC43816

Gene: lacZ AIK79510.1 Structure source: AlphaFold + ColabFold UniProt A0A085DPL4
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Amino acids 1035
Annotations 10
Features 48
PDB binders 11
Druggability 0.744

Overview

Basic information about this protein and its source genome.

Accession
VK055_0887
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
lacZ AIK79510.1
Status
annotated
Amino acids
1035
Structure source
AlphaFold + ColabFold
EC
3.2.1.23
GO
GO:0030246 Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. 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:0004565 Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides. GO:0009341 A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species. GO:0004553 Catalysis of the hydrolysis of any O-glycosyl bond.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
23.516
Human E-value
1.03e-19
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Unknown
ColabFold pLDDT
96.09

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 0.744
Structure A0A085DPL4
Pocket Pocket 6
P2Rank 0.905
Structure A0A085DPL4
Pocket Pocket 1
ColabFold model
FPocket 0.648 · Pocket 1
P2Rank 0.92 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 98 / 4744 genomes with a hit
Normalized 0.021

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0030246 Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • 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:0004565 Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
  • GO:0009341 A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.
  • GO:0004553 Catalysis of the hydrolysis of any O-glycosyl bond.
  • GO:0016798 Catalysis of the hydrolysis of any glycosyl bond.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0005990 The chemical reactions and pathways resulting in the breakdown of lactose, the disaccharide galactopyranosyl-glucose.

Sequence Features

Domain/signature hits from InterPro and related databases.

48 records
Show feature table
Start End DB Term Name
227 341 Gene3D G3DSA:2.60.40.10 Immunoglobulins
227 341 InterPro IPR013783 Immunoglobulin-like fold
17 1033 PANTHER PTHR46323 BETA-GALACTOSIDASE
629 738 SUPERFAMILY SSF49303 beta-Galactosidase/glucuronidase domain
629 738 InterPro IPR036156 Beta-Galactosidase/glucuronidase domain superfamily
342 632 FunFam G3DSA:3.20.20.80:FF:000018 Beta-galactosidase
59 225 Pfam PF02837 Glycosyl hydrolases family 2, sugar binding domain
59 225 InterPro IPR006104 Glycosyl hydrolases family 2, sugar binding domain
228 341 SUPERFAMILY SSF49303 beta-Galactosidase/glucuronidase domain
228 341 InterPro IPR036156 Beta-Galactosidase/glucuronidase domain superfamily
342 632 Gene3D G3DSA:3.20.20.80 Glycosidases
455 469 ProSitePatterns PS00608 Glycosyl hydrolases family 2 acid/base catalyst.
455 469 InterPro IPR023232 Glycoside hydrolase, family 2, active site
539 554 PRINTS PR00132 Glycosyl hydrolase family 2 signature
539 554 InterPro IPR006101 Glycoside hydrolase, family 2
352 366 PRINTS PR00132 Glycosyl hydrolase family 2 signature
352 366 InterPro IPR006101 Glycoside hydrolase, family 2
153 168 PRINTS PR00132 Glycosyl hydrolase family 2 signature
153 168 InterPro IPR006101 Glycoside hydrolase, family 2
455 470 PRINTS PR00132 Glycosyl hydrolase family 2 signature
455 470 InterPro IPR006101 Glycoside hydrolase, family 2
383 401 PRINTS PR00132 Glycosyl hydrolase family 2 signature
383 401 InterPro IPR006101 Glycoside hydrolase, family 2
766 1031 Pfam PF02929 Beta galactosidase small chain
766 1031 InterPro IPR004199 Beta galactosidase small chain/ domain 5
760 1033 SMART SM01038 Bgal_small_N_2
760 1033 InterPro IPR004199 Beta galactosidase small chain/ domain 5
343 632 SUPERFAMILY SSF51445 (Trans)glycosidases
343 632 InterPro IPR017853 Glycoside hydrolase superfamily
11 225 Gene3D G3DSA:2.60.120.260 -
12 1035 Hamap MF_01687 Beta-galactosidase [lacZ].
12 1035 InterPro IPR023933 Glycoside hydrolase, family 2, beta-galactosidase
633 741 Gene3D G3DSA:2.60.40.10 Immunoglobulins
633 741 InterPro IPR013783 Immunoglobulin-like fold
21 225 SUPERFAMILY SSF49785 Galactose-binding domain-like
21 225 InterPro IPR008979 Galactose-binding-like domain superfamily
393 418 ProSitePatterns PS00719 Glycosyl hydrolases family 2 signature 1.
393 418 InterPro IPR023230 Glycoside hydrolase, family 2, conserved site
647 735 Pfam PF16353 Beta-galactosidase, domain 4
647 735 InterPro IPR032312 Beta-galactosidase, domain 4
230 341 Pfam PF00703 Glycosyl hydrolases family 2
230 341 InterPro IPR006102 Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich
744 1034 Gene3D G3DSA:2.70.98.10 -
744 1034 InterPro IPR014718 Glycoside hydrolase-type carbohydrate-binding
343 636 Pfam PF02836 Glycosyl hydrolases family 2, TIM barrel domain
343 636 InterPro IPR006103 Glycoside hydrolase family 2, catalytic domain
745 1033 SUPERFAMILY SSF74650 Galactose mutarotase-like
745 1033 InterPro IPR011013 Galactose mutarotase-like domain superfamily

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_A0A085DPL4
AlphaFold — — full sequence — Viewing
ColabFold VK055_0887
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
6 0.744
10 0.737
1 0.252
32 0.206

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 16.88 0.79
2 6.55 0.331
3 6.47 0.327
4 6.39 0.322
5 3.83 0.149

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.

67 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
149
3CZJ
P00722 178.1 Da LogP -3.01 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@@H]1[C@@H]([C@@H]([C@H](C(=O)O1)O)O)O)O
2DG
4DUV
P00722 164.2 Da LogP -2.19 TPSA 90.2 ✓ Ro5 ✓ Clean C1[C@H]([C@H]([C@H](O[C@@H]1O)CO)O)O
BTB
4DUV
P00722 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
DGJ
6TSH
P00722 163.2 Da LogP -2.97 TPSA 93.0 ✓ Ro5 ✓ Clean C1[C@@H]([C@H]([C@H]([C@H](N1)CO)O)O)O
DVL
6KUZ
P00722 537.6 Da LogP 2.84 TPSA 138.6 1 viol. ✓ Clean Cc1cc(c(c(c1)c2nc3ccccc3s2)OCc4ccc(cc4)O[C@H]5[…
F4X
7BRS
P00722 568.7 Da LogP 3.38 TPSA 139.7 1 viol. ✓ Clean CC1(c2ccccc2[N+](=C1/C=C/c3ccc(cc3)O[C@H]4[C@@H…
F6L
7BTK
P00722 560.6 Da LogP 2.85 TPSA 139.7 1 viol. ✓ Clean CC1(c2ccccc2[N+](=C1/C=C/c3ccc(cc3)O[C@H]4[C@@H…
GIF
5T99
A0A2D0TCC8 147.2 Da LogP -2.08 TPSA 72.7 ✓ Ro5 ✓ Clean C1[C@@H]([C@@H]([C@@H](CN1)O)O)CO
GTZ
1JZ6
P00722 202.2 Da LogP -3.02 TPSA 124.5 ✓ Ro5 ✓ Clean C([C@@H]1[C@@H]([C@@H]([C@H](c2n1nnn2)O)O)O)O
MLI
6SE8
A0A023UGN9 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PTQ
5A1A
P00722 300.4 Da LogP -0.24 TPSA 90.2 ✓ Ro5 ✓ Clean c1ccc(cc1)CCS[C@H]2[C@@H]([C@H]([C@H]([C@H](O2)…

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.