Protein profile

KP13_01719

ATP-dependent DNA helicase recQ

Genome: KpKP13

Gene: recQ AHE46977.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GKF3
Amino acids 608
Annotations 19
Features 48
PDB binders 4
Druggability 0.635

Overview

Basic information about this protein and its source genome.

Accession
KP13_01719
Gene
recQ AHE46977.1
Status
annotated
Amino acids
608
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
55.102
Human E-value
7.66e-13
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
63.744
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
89.38

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 0.635
Structure A0A0H3GKF3
Pocket Pocket 10
P2Rank 0.948
Structure A0A0H3GKF3
Pocket Pocket 1
ColabFold model
FPocket 0.843 · Pocket 10
P2Rank 0.862 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 140 / 4744 genomes with a hit
Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 18 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

18
  • GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.
  • GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
  • 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:0043138 Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis.
  • GO:0009432 An error-prone process for repairing damaged microbial DNA.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
  • GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0043590 The region of a bacterial cell to which the DNA is confined.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0030894 A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0009378 Unwinding a DNA helix of DNA containing four-way junctions, including Holliday junctions, driven by ATP hydrolysis.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

48 records
Show feature table
Start End DB Term Name
529 608 ProSiteProfiles PS50967 HRDC domain profile.
529 608 InterPro IPR002121 HRDC domain
2 208 Gene3D G3DSA:3.40.50.300 -
2 208 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
341 522 Gene3D G3DSA:1.10.10.10 -
341 522 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
223 371 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile.
223 371 InterPro IPR001650 Helicase, C-terminal
8 201 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
8 201 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
28 187 Pfam PF00270 DEAD/DEAH box helicase
28 187 InterPro IPR011545 DEAD/DEAH box helicase domain
529 608 SMART SM00341 hrdc7
1 209 FunFam G3DSA:3.40.50.300:FF:000296 ATP-dependent DNA helicase RecQ
526 606 FunFam G3DSA:1.10.150.80:FF:000002 ATP-dependent DNA helicase RecQ
530 605 SUPERFAMILY SSF47819 HRDC-like
530 605 InterPro IPR010997 HRDC-like superfamily
210 340 FunFam G3DSA:3.40.50.300:FF:000156 ATP-dependent DNA helicase recQ
13 592 PANTHER PTHR13710 DNA HELICASE RECQ FAMILY MEMBER
15 464 NCBIfam TIGR00614 RecQ family ATP-dependent DNA helicase
15 464 InterPro IPR004589 DNA helicase, ATP-dependent, RecQ type
210 340 CDD cd18794 SF2_C_RecQ
34 202 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
34 202 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
523 608 Gene3D G3DSA:1.10.150.80 HRDC domain
523 608 InterPro IPR044876 HRDC domain superfamily
223 330 Pfam PF00271 Helicase conserved C-terminal domain
223 330 InterPro IPR001650 Helicase, C-terminal
533 599 Pfam PF00570 HRDC domain
533 599 InterPro IPR002121 HRDC domain
343 404 Pfam PF16124 RecQ zinc-binding
343 404 InterPro IPR032284 ATP-dependent DNA helicase RecQ, zinc-binding domain
406 514 Pfam PF09382 RQC domain
406 514 InterPro IPR018982 RQC domain
22 218 SMART SM00487 ultradead3
22 218 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
411 514 SMART SM00956 RQC_2
411 514 InterPro IPR018982 RQC domain
14 209 CDD cd17920 DEXHc_RecQ
13 601 NCBIfam TIGR01389 DNA helicase RecQ
13 601 InterPro IPR006293 DNA helicase, ATP-dependent, RecQ type, bacterial
209 340 Gene3D G3DSA:3.40.50.300 -
209 340 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
341 522 FunFam G3DSA:1.10.10.10:FF:000175 ATP-dependent DNA helicase RecQ
250 331 SMART SM00490 helicmild6
250 331 InterPro IPR001650 Helicase, C-terminal
208 455 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
208 455 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase

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_A0A0H3GKF3
AlphaFold full sequence Viewing
ColabFold KP13_01719
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
10 0.635

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 22.06 0.877
2 4.79 0.212
3 2.42 0.065
4 1.23 0.011
5 1.0 0.006

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.

78 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
6SV O94762 226.3 Da LogP 1.80 TPSA 50.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NC(=O)NC[C@H]2CCCO2
AGS P15043 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP O01378 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
EU3 Q14191 152.0 Da LogP 0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Eu+3]

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.