Protein profile

VK055_3534

alpha amylase, catalytic domain protein

Genome: KpATCC43816

Gene: AIK82090.1 Structure source: Experimental + ColabFold UniProt Q9RHR1
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Amino acids 610
Annotations 8
Features 13
PDB binders 5
Druggability 0.846

Overview

Basic information about this protein and its source genome.

Accession
VK055_3534
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82090.1
Status
annotated
Amino acids
610
Structure source
Experimental + ColabFold
EC
3.2.1.98
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:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria). GO:0004556 Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units. GO:0005509 Binding to a calcium ion (Ca2+). GO:0033927 Catalysis of the hydrolysis of (1->4)-alpha-D-glucosidic linkages in amylaceous polysaccharides, to remove successive maltohexaose residues from the non-reducing chain ends. GO:0030980 The chemical reactions and pathways resulting in the breakdown of alpha-glucans.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
27.957
Human E-value
7.87e-06
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
39.362
Localization
Periplasmic
ColabFold pLDDT
94.2

Selected Druggability evidence

PDB experimental structure

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 0.846
Structure 9US4
Pocket Pocket 1
P2Rank 0.958
Structure 9US3
Pocket Pocket 1
ColabFold model
FPocket 0.522 · Pocket 40
P2Rank 0.949 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 82 / 4744 genomes with a hit
Normalized 0.017

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:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
  • GO:0004556 Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units.
  • GO:0005509 Binding to a calcium ion (Ca2+).
  • GO:0033927 Catalysis of the hydrolysis of (1->4)-alpha-D-glucosidic linkages in amylaceous polysaccharides, to remove successive maltohexaose residues from the non-reducing chain ends.
  • GO:0030980 The chemical reactions and pathways resulting in the breakdown of alpha-glucans.
  • GO:0009313 The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
109 350 Gene3D G3DSA:3.20.20.80 Glycosidases
126 570 SMART SM00642 aamy
126 570 InterPro IPR006047 Glycosyl hydrolase, family 13, catalytic domain
109 348 FunFam G3DSA:3.20.20.80:FF:000089 Periplasmic alpha-amylase
112 579 SUPERFAMILY SSF51445 (Trans)glycosidases
112 579 InterPro IPR017853 Glycoside hydrolase superfamily
362 575 FunFam G3DSA:3.20.20.80:FF:000079 Alpha-amylase
109 604 PANTHER PTHR10357 ALPHA-AMYLASE FAMILY MEMBER
355 577 Gene3D G3DSA:3.20.20.80 Glycosidases
159 302 Pfam PF00128 Alpha amylase, catalytic domain
159 302 InterPro IPR006047 Glycosyl hydrolase, family 13, catalytic domain
373 527 Pfam PF00128 Alpha amylase, catalytic domain
373 527 InterPro IPR006047 Glycosyl hydrolase, family 13, catalytic domain

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

4 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 9US3
X-ray 1.90 Å A,B
97.2% 18-610
PDBe RCSB PDBj File
Viewing
PDB 9US4
X-ray 1.95 Å A,B
97.2% 18-610
PDBe RCSB PDBj File
Loaded
PDB 9US5
X-ray 2.66 Å A
80.5% 120-610
PDBe RCSB PDBj File
Loaded
PDB 9US6
X-ray 2.70 Å A,B
97.2% 18-610
PDBe RCSB PDBj File
Loaded
ColabFold VK055_3534
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
33 0.384
6 0.219
60 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 51.73 0.982
2 48.02 0.977
3 8.28 0.441
4 6.7 0.341
5 4.23 0.173

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.

12 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
ABC
7TAA
P0C1B3 937.9 Da LogP -10.86 TPSA 439.0 3 viol. ✓ Clean C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@…
ACI
2CXG
P43379 175.2 Da LogP -2.67 TPSA 106.9 ✓ Ro5 ✓ Clean C1=C([C@H]([C@@H]([C@H]([C@H]1N)O)O)O)CO
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@…
FLC
6WNI
U5CJP3 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
NOJ
1I75
P05618 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

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.