Protein target profile

PA3777

exodeoxyribonuclease VII large subunit

Genome: NC_002516.2

Gene: PA3777 xseA 3D evidence: AlphaFold DB model UniProt Q9HXL8
Export view
Length 459
Pocket druggability 0.724
EC / GO 1 / 5
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

4 signals

Strengths

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 0.72. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model

Risks / watch

No major risk signal surfaced in the loaded evidence.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
How to read this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal TPW pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Overview

Basic information about this protein and its source genome.

Accession
PA3777
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3777 xseA
Status
annotated
Amino acids
459
3D evidence
AlphaFold DB model
EC
3.1.11.6
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0009318 An enzyme complex that catalyzes exonucleolytic cleavage in either 5' to 3' or 3' to 5' direction to yield nucleoside 5'-phosphates; it prefers single-stranded DNA. GO:0008855 Catalysis of the exonucleolytic cleavage in either 5' to 3' or 3' to 5' direction to yield 5'-phosphomononucleotides. GO:0003676 Binding to a nucleic acid. GO:0006308 The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected pocket evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.724
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MRNDPFQRLGLDREVLTVSQLNQRARLLLEDVFPQVWVEGELSNLARPASGHVYFTLKDSNAQIRCALFRQNALRVRQALRDGLAVKVRGKISLFEGRGDYQLIADTVEPAGDGALRLAFEALKEKLAGEGLFASERKRPLPAHPRRIGIVSSPSGAVIRDIISVFRRRAPQVELTLVPTAVQGREAVAQIVRALQLADRQGFDALILARGGGSLEDLWCFNEEAVARAVAACATPIVSAVGHETDVSISDFVADVRAPTPSAAAELLAPNAGDLQQRLDGLRRRLVLRMRDQLLRERLRLEGVARRLRHPGERLRQQAQRLDDLDMRLRRAFERQLAVRHERLVRLETRLAAQHPGRTLALLRQKLDSLAARLPRAAREVLKDRRQRLEGLAQTLNVVSPLATLGRGYSILLDERGRAIRDAGQTQPGQRLKARLAEGELEVRVEDNHRTPVTLSLLD

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009318 An enzyme complex that catalyzes exonucleolytic cleavage in either 5' to 3' or 3' to 5' direction to yield nucleoside 5'-phosphates; it prefers single-stranded DNA.
  • GO:0008855 Catalysis of the exonucleolytic cleavage in either 5' to 3' or 3' to 5' direction to yield 5'-phosphomononucleotides.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0006308 The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
360 380 Coils Coil Coil
132 443 Pfam PF02601 Exonuclease VII, large subunit
132 443 InterPro IPR020579 Exonuclease VII, large subunit, C-terminal
315 335 Coils Coil Coil
17 360 NCBIfam TIGR00237 exodeoxyribonuclease VII large subunit
17 360 InterPro IPR003753 Exonuclease VII, large subunit
12 450 PANTHER PTHR30008 EXODEOXYRIBONUCLEASE 7 LARGE SUBUNIT
12 450 InterPro IPR003753 Exonuclease VII, large subunit
16 108 Pfam PF13742 OB-fold nucleic acid binding domain
16 108 InterPro IPR025824 OB-fold nucleic acid binding domain
13 446 Hamap MF_00378 Exodeoxyribonuclease 7 large subunit [xseA].
13 446 InterPro IPR003753 Exonuclease VII, large subunit
35 112 CDD cd04489 ExoVII_LU_OBF
35 112 InterPro IPR025824 OB-fold nucleic acid binding domain

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

3D visualization script Full viewer

Loading 3D structure...

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Structural evidence

0 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB PA3777
AlphaFold DB — — full sequence — Viewing
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
1 0.724
2 0.368
4 0.281