Protein profile

KP13_02293

Exodeoxyribonuclease V beta chain

Genome: KpKP13

Gene: AHE42864.1 recB Structure source: AlphaFold + ColabFold UniProt A0A0H3GSM0
Amino acids 1178
Annotations 14
Features 33
PDB binders 2
Druggability 0.499

Overview

Basic information about this protein and its source genome.

Accession
KP13_02293
Gene
AHE42864.1 recB
Status
annotated
Amino acids
1178
Structure source
AlphaFold + ColabFold

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 (%)
75.424
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
90.05

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 0.499
Structure A0A0H3GSM0
Pocket Pocket 5
P2Rank 0.789
Structure A0A0H3GSM0
Pocket Pocket 1
ColabFold model
FPocket 0.227 · Pocket 100
P2Rank 0.809 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 110 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 12 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

12
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
  • GO:0008854 Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides.
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0009338 An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA.
  • GO:0043138 Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0000724 The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
19 826 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
19 826 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
480 746 ProSiteProfiles PS51217 UvrD-like DNA helicase C-terminal domain profile.
480 746 InterPro IPR014017 UvrD-like DNA helicase, C-terminal
886 1177 Gene3D G3DSA:3.90.320.10 -
886 1177 InterPro IPR011604 PD-(D/E)XK endonuclease-like domain superfamily
2 450 ProSiteProfiles PS51198 UvrD-like DNA helicase ATP-binding domain profile.
2 450 InterPro IPR014016 UvrD-like helicase, ATP-binding domain
947 1140 Pfam PF12705 PD-(D/E)XK nuclease superfamily
947 1140 InterPro IPR038726 PD-(D/E)XK endonuclease-like domain, AddAB-type
8 1169 NCBIfam TIGR00609 exodeoxyribonuclease V subunit beta
8 1169 InterPro IPR004586 RecBCD enzyme subunit RecB
898 1166 CDD cd22352 RecB_C-like
15 436 Pfam PF00580 UvrD/REP helicase N-terminal domain
15 436 InterPro IPR014016 UvrD-like helicase, ATP-binding domain
215 235 Coils Coil Coil
886 1176 FunFam G3DSA:3.90.320.10:FF:000003 RecBCD enzyme subunit RecB
8 436 Gene3D G3DSA:3.40.50.300 -
8 436 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
896 1171 SUPERFAMILY SSF52980 Restriction endonuclease-like
896 1171 InterPro IPR011335 Restriction endonuclease type II-like
736 816 CDD cd18807 SF1_C_UvrD
5 1170 Hamap MF_01485 RecBCD enzyme subunit RecB [recB].
5 1170 InterPro IPR004586 RecBCD enzyme subunit RecB
19 833 PANTHER PTHR11070 UVRD / RECB / PCRA DNA HELICASE FAMILY MEMBER
19 833 InterPro IPR000212 DNA helicase, UvrD/REP type
583 728 Gene3D G3DSA:1.10.486.10 PCRA; domain 4
445 843 Gene3D G3DSA:3.40.50.300 -
445 843 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
782 809 Coils Coil Coil
155 349 Gene3D G3DSA:1.10.3170.10 Recbcd, chain B, domain 2
441 809 Pfam PF13361 UvrD-like helicase C-terminal domain
441 809 InterPro IPR014017 UvrD-like DNA helicase, C-terminal

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_A0A0H3GSM0
AlphaFold full sequence Viewing
ColabFold KP13_02293
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
5 0.499

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 13.9 0.703
2 12.49 0.653
3 8.77 0.469
4 5.34 0.253
5 5.06 0.231

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
ANP P03018 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)…
MGF P03018 81.3 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean F[Mg-](F)F

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.