Protein profile

VK055_0125

DEAD/DEAH box helicase family protein

Genome: KpATCC43816

Gene: AIK78753.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVB5
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Amino acids 636
Annotations 12
Features 22
PDB binders 3
Druggability 0.57

Overview

Basic information about this protein and its source genome.

Accession
VK055_0125
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK78753.1
Status
annotated
Amino acids
636
Structure source
AlphaFold + ColabFold
EC
5.6.2.3
GO
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0003676 Binding to a nucleic acid. GO:0016818 Catalysis of the hydrolysis of any acid anhydride which contains phosphorus. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0006139 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. 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 (%)
61.367
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
88.27

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 0.57
Structure A0A0H3GVB5
Pocket Pocket 16
P2Rank 0.888
Structure A0A0H3GVB5
Pocket Pocket 1
ColabFold model
FPocket 0.831 · Pocket 24
P2Rank 0.874 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 136 / 4744 genomes with a hit
Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0016818 Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0006139 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
  • GO:0043139 Unwinding a DNA helix in the 5' to 3' direction, driven by ATP hydrolysis.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0046872 Binding to a metal ion.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
13 232 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
13 232 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
18 283 Gene3D G3DSA:3.40.50.300 -
18 283 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
18 605 PANTHER PTHR11472 DNA REPAIR DEAD HELICASE RAD3/XP-D SUBFAMILY MEMBER
18 605 InterPro IPR045028 Helicase superfamily 1/2, DinG/Rad3-like
16 314 SMART SM00487 ultradead3
16 314 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
439 627 FunFam G3DSA:3.40.50.300:FF:000466 ATP-dependent DNA helicase
40 596 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
40 596 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
18 283 FunFam G3DSA:3.40.50.300:FF:000499 ATP-dependent DNA helicase
444 626 Gene3D G3DSA:3.40.50.300 -
444 626 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
10 272 ProSiteProfiles PS51193 Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile.
10 272 InterPro IPR014013 Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type
474 603 SMART SM00491 Cxpdneu3
474 603 InterPro IPR006555 ATP-dependent helicase, C-terminal
18 232 Pfam PF04851 Type III restriction enzyme, res subunit
18 232 InterPro IPR006935 Helicase/UvrB, N-terminal
459 616 Pfam PF13307 Helicase C-terminal domain
459 616 InterPro IPR006555 ATP-dependent 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

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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_A0A0H3GVB5
AlphaFold — — full sequence — Viewing
ColabFold VK055_0125
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
9 0.042
51 0.007
1 0.002
3 0.0

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 28.23 0.888
2 10.09 0.467
3 9.05 0.416
4 6.21 0.257
5 5.55 0.22

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.

3 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
BEF
6FWS
P27296 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
FC6
3CRW
Q4JC68 212.0 Da LogP 0.10 TPSA 142.7 ✓ Ro5 ✓ Clean C(#N)[Fe](C#N)(C#N)(C#N)(C#N)C#N
FLC
3CRV
Q4JC68 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=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.