Protein profile

KP13_01714

DNA helicase II

Genome: KpKP13

Gene: AHE46982.1 uvrD Structure source: AlphaFold + ColabFold UniProt A0A0H3GGJ9
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Amino acids 720
Annotations 14
Features 26
PDB binders 2
Druggability 0.038

Overview

Basic information about this protein and its source genome.

Accession
KP13_01714
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46982.1 uvrD
Status
annotated
Amino acids
720
Structure source
AlphaFold + ColabFold
EC
5.6.2.4
GO
GO:0006268 OBSOLETE. The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis. 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).

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 (%)
95.972
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
87.83

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 0.038
Structure A0A0H3GGJ9
Pocket Pocket 33
P2Rank 0.649
Structure A0A0H3GGJ9
Pocket Pocket 1
ColabFold model
FPocket 0.446 · Pocket 29
P2Rank 0.683 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 165 / 4744 genomes with a hit
Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

13
  • GO:0006268 OBSOLETE. The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
  • 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:0033202 A protein complex that possesses DNA helicase activity.
  • 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:0042802 Binding to an identical protein or proteins.
  • 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:0000725 A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
281 636 Gene3D G3DSA:3.40.50.300 -
281 636 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
8 286 ProSiteProfiles PS51198 UvrD-like DNA helicase ATP-binding domain profile.
8 286 InterPro IPR014016 UvrD-like helicase, ATP-binding domain
114 187 FunFam G3DSA:1.10.10.160:FF:000002 DNA helicase
114 187 Gene3D G3DSA:1.10.10.160 -
114 187 InterPro IPR013986 DExx box DNA helicase domain superfamily
280 383 FunFam G3DSA:3.40.50.300:FF:001201 ATP-dependent DNA helicase UvrD2
287 564 ProSiteProfiles PS51217 UvrD-like DNA helicase C-terminal domain profile.
287 564 InterPro IPR014017 UvrD-like DNA helicase, C-terminal
10 271 Pfam PF00580 UvrD/REP helicase N-terminal domain
10 271 InterPro IPR014016 UvrD-like helicase, ATP-binding domain
7 642 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
7 642 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
6 718 NCBIfam TIGR01075 DNA helicase UvrD
6 718 InterPro IPR005753 DNA helicase, ATP-dependent, UvrD type
9 647 PANTHER PTHR11070 UVRD / RECB / PCRA DNA HELICASE FAMILY MEMBER
9 647 InterPro IPR000212 DNA helicase, UvrD/REP type
10 274 Gene3D G3DSA:3.40.50.300 -
10 274 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
285 614 CDD cd18807 SF1_C_UvrD
382 538 FunFam G3DSA:1.10.486.10:FF:000001 DNA helicase
382 538 Gene3D G3DSA:1.10.486.10 PCRA; domain 4
277 616 Pfam PF13361 UvrD-like helicase C-terminal domain
277 616 InterPro IPR014017 UvrD-like DNA helicase, C-terminal
11 283 CDD cd17932 DEXQc_UvrD

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_A0A0H3GGJ9
AlphaFold — — full sequence — Viewing
ColabFold KP13_01714
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 8.6 0.46
2 7.85 0.416
3 4.02 0.16
4 1.92 0.039
5 1.9 0.038

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
2IS4
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
2IS6
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.