Protein profile

KP13_01795

DNA polymerase III subunit alpha

Genome: KpKP13

Gene: AHE46235.1 dnaE Structure source: AlphaFold + ColabFold UniProt A0A0H3GS50
Export view
Amino acids 1160
Annotations 7
Features 30
PDB binders 2
Druggability 0.598

Overview

Basic information about this protein and its source genome.

Accession
KP13_01795
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46235.1 dnaE
Status
annotated
Amino acids
1160
Structure source
AlphaFold + ColabFold
EC
2.7.7.7
GO
GO:0003676 Binding to a nucleic acid. GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. 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:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0003887 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time.

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 (%)
95.431
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
90.56

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 0.598
Structure A0A0H3GS50
Pocket Pocket 64
P2Rank 0.778
Structure A0A0H3GS50
Pocket Pocket 1
ColabFold model
FPocket 0.437 · Pocket 78
P2Rank 0.894 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 159 / 4744 genomes with a hit
Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0003676 Binding to a nucleic acid.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
  • 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:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0003887 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
980 1074 Gene3D G3DSA:2.40.50.140 -
980 1074 InterPro IPR012340 Nucleic acid-binding, OB-fold
713 886 Gene3D G3DSA:1.10.150.870 -
433 510 FunFam G3DSA:1.10.10.1600:FF:000001 DNA polymerase III subunit alpha
1 270 Gene3D G3DSA:3.20.20.140 -
5 281 CDD cd07433 PHP_PolIIIA_DnaE1
713 886 FunFam G3DSA:1.10.150.870:FF:000001 DNA polymerase III subunit alpha
6 263 SUPERFAMILY SSF89550 PHP domain-like
6 263 InterPro IPR016195 Polymerase/histidinol phosphatase-like
980 1073 FunFam G3DSA:2.40.50.140:FF:000106 DNA polymerase III subunit alpha
1 270 FunFam G3DSA:3.20.20.140:FF:000028 DNA polymerase III subunit alpha
8 170 Pfam PF02811 PHP domain
8 170 InterPro IPR004013 PHP domain
433 510 Gene3D G3DSA:1.10.10.1600 Bacterial DNA polymerase III alpha subunit, thumb domain
433 510 InterPro IPR041931 Bacterial DNA polymerase III alpha subunit, thumb domain
995 1080 CDD cd04485 DnaE_OBF
808 897 Pfam PF14579 Helix-hairpin-helix motif
808 897 InterPro IPR029460 DNA polymerase, helix-hairpin-helix motif
6 1031 NCBIfam TIGR00594 DNA polymerase III subunit alpha
6 1031 InterPro IPR004805 Error-prone DNA polymerase/DNA polymerase III subunit alpha DnaE/PolC
7 74 SMART SM00481 npolultra
7 74 InterPro IPR003141 Polymerase/histidinol phosphatase, N-terminal
1000 1072 Pfam PF01336 OB-fold nucleic acid binding domain
1000 1072 InterPro IPR004365 OB-fold nucleic acid binding domain, AA-tRNA synthetase-type
292 558 Pfam PF07733 Bacterial DNA polymerase III alpha NTPase domain
292 558 InterPro IPR011708 Bacterial DNA polymerase III, alpha subunit, NTPase domain
561 735 Pfam PF17657 Bacterial DNA polymerase III alpha subunit finger domain
561 735 InterPro IPR040982 DNA polymerase III alpha subunit finger domain
6 1156 PANTHER PTHR32294 DNA POLYMERASE III SUBUNIT ALPHA
6 1156 InterPro IPR004805 Error-prone DNA polymerase/DNA polymerase III subunit alpha DnaE/PolC

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

Loading 3D structure...

Legend High Medium Low

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_A0A0H3GS50
AlphaFold — — full sequence — Viewing
ColabFold KP13_01795
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
64 0.598
38 0.207

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 16.6 0.782
2 12.53 0.654
3 5.34 0.252
4 2.8 0.086
5 2.68 0.079

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.

52 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
3PO
2HPM
Q9XDH5 258.0 Da LogP -0.69 TPSA 170.8 ✓ Ro5 ✓ Clean OP(=O)(O)OP(=O)(O)OP(=O)(O)O
DTP
3E0D
Q9XDH5 491.2 Da LogP -0.60 TPSA 258.9 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@]…

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.