Protein profile

KP13_00389

Replicative DNA helicase

Genome: KpKP13

Gene: dnaB AHE46873.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ64
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Amino acids 471
Annotations 11
Features 23
PDB binders 7
Druggability 0.535

Overview

Basic information about this protein and its source genome.

Accession
KP13_00389
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
dnaB AHE46873.1
Status
annotated
Amino acids
471
Structure source
AlphaFold + ColabFold
EC
5.6.2.3
GO
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: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: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.

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 (%)
98.514
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
89.27

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 0.535
Structure A0A0H3GQ64
Pocket Pocket 14
P2Rank 0.085
Structure A0A0H3GQ64
Pocket Pocket 1
ColabFold model
FPocket 0.598 · Pocket 17
P2Rank 0.269 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 203 / 4744 genomes with a hit
Normalized 0.043

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • 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: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: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:1990077 Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart.
  • GO:0043139 Unwinding a DNA helix in the 5' to 3' direction, driven by ATP hydrolysis.
  • GO:0042802 Binding to an identical protein or proteins.
  • GO:0006269 The synthesis of a short nucleotide polymer using one strand of unwound DNA as a template. The product is usually a RNA molecule between 4-15 nucleotides long that provides a free 3'-OH that can be extended by DNA-directed DNA polymerases. In certain conditions, for example in response to DNA damage, some primases synthesize a DNA primer.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
21 183 Gene3D G3DSA:1.10.860.10 DNAb Helicase; Chain A
21 183 InterPro IPR016136 DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal
25 136 SUPERFAMILY SSF48024 N-terminal domain of DnaB helicase
25 136 InterPro IPR036185 DNA helicase, DnaB-like, N-terminal domain superfamily
1 25 MobiDBLite mobidb-lite consensus disorder prediction
27 128 Pfam PF00772 DnaB-like helicase N terminal domain
27 128 InterPro IPR007693 DNA helicase, DnaB-like, N-terminal
206 462 Pfam PF03796 DnaB-like helicase C terminal domain
206 462 InterPro IPR007694 DNA helicase, DnaB-like, C-terminal
24 466 PANTHER PTHR30153 REPLICATIVE DNA HELICASE DNAB
184 463 Gene3D G3DSA:3.40.50.300 -
184 463 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
27 464 NCBIfam TIGR00665 replicative DNA helicase
27 464 InterPro IPR007692 DNA helicase, DnaB type
206 462 CDD cd00984 DnaB_C
223 429 SMART SM00382 AAA_5
223 429 InterPro IPR003593 AAA+ ATPase domain
20 183 FunFam G3DSA:1.10.860.10:FF:000002 Replicative DNA helicase
185 468 FunFam G3DSA:3.40.50.300:FF:000076 Replicative DNA helicase
200 467 ProSiteProfiles PS51199 Superfamily 4 helicase domain profile.
200 467 InterPro IPR007694 DNA helicase, DnaB-like, C-terminal
204 456 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
204 456 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_A0A0H3GQ64
AlphaFold — — full sequence — Viewing
ColabFold KP13_00389
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
14 0.535

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 1.64 0.027
2 0.84 0.003

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.

57 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
08T
6QEM
P0ACB0 — — — [Be](OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@…
ALF
4ESV
Q9X4C9 103.0 Da LogP 1.30 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al-](F)(F)F
ANP
1E0J
P03692 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)…
DTP
1CR2
P03692 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@]…
FLC
4A1F
O25916 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
TTP
1CR1
P03692 482.2 Da LogP -1.16 TPSA 244.1 2 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…
TYD
1CR4
P03692 402.2 Da LogP -1.28 TPSA 197.6 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)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.