Protein profile

PA3138

excinuclease ABC subunit B

Genome: NC_002516.2

Gene: PA3138 uvrB Structure source: AlphaFold UniProt P72174
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Amino acids 670
Annotations 11
Features 45
PDB binders 9
Druggability 0.523

Overview

Basic information about this protein and its source genome.

Accession
PA3138
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3138 uvrB
Status
annotated
Amino acids
670
Structure source
AlphaFold
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0009380 Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0009381 Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid at sites flanking regions of damaged DNA to which the Uvr ABC excinuclease complexes bind.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
35.802
Human E-value
6.1e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.523
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

11 GO

Gene Ontology (GO)

11
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009380 Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0009381 Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid at sites flanking regions of damaged DNA to which the Uvr ABC excinuclease complexes bind.
  • GO:0000715 The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix.
  • GO:0009432 An error-prone process for repairing damaged microbial DNA.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0006289 A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
  • GO:0005515 Binding to a protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

45 records
Show feature table
Start End DB Term Name
646 670 Coils Coil Coil
11 118 Pfam PF04851 Type III restriction enzyme, res subunit
11 118 InterPro IPR006935 Helicase/UvrB, N-terminal
8 424 SMART SM00487 ultradead3
8 424 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
321 409 Gene3D G3DSA:3.40.50.300 -
321 409 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
3 664 NCBIfam TIGR00631 excinuclease ABC subunit UvrB
3 664 InterPro IPR004807 UvrABC system, subunit B
256 283 Coils Coil Coil
550 592 Pfam PF12344 Ultra-violet resistance protein B
550 592 InterPro IPR024759 UvrB, YAD/RRR-motif-containing domain
429 582 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile.
429 582 InterPro IPR001650 Helicase, C-terminal
418 588 CDD cd18790 SF2_C_UvrB
158 248 Pfam PF17757 UvrB interaction domain
158 248 InterPro IPR041471 UvrB, interaction domain
3 668 PANTHER PTHR24029 UVRABC SYSTEM PROTEIN B
3 668 InterPro IPR004807 UvrABC system, subunit B
626 669 Gene3D G3DSA:4.10.860.10 UVR domain
4 412 CDD cd17916 DEXHc_UvrB
2 237 Gene3D G3DSA:3.40.50.300 -
2 237 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
435 542 Pfam PF00271 Helicase conserved C-terminal domain
435 542 InterPro IPR001650 Helicase, C-terminal
36 581 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
36 581 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
25 158 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
25 158 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
632 665 Pfam PF02151 UvrB/uvrC motif
632 665 InterPro IPR001943 UVR domain
2 666 Hamap MF_00204 UvrABC system protein B [uvrB].
2 666 InterPro IPR004807 UvrABC system, subunit B
412 588 Gene3D G3DSA:3.40.50.300 -
412 588 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
249 314 Gene3D G3DSA:6.10.140.240 -
631 666 ProSiteProfiles PS50151 UVR domain profile.
631 666 InterPro IPR001943 UVR domain
229 412 FunFam G3DSA:3.40.50.300:FF:000477 UvrABC system protein B
626 667 SUPERFAMILY SSF46600 C-terminal UvrC-binding domain of UvrB
626 667 InterPro IPR036876 UVR domain superfamily
458 544 SMART SM00490 helicmild6
458 544 InterPro IPR001650 Helicase, C-terminal
2 413 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
2 413 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.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA3138
AlphaFold — — 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
2 0.205

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.

102 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
AF3
3EX7
P38919 84.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al](F)F
ANP
2HYI
P38919 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)…
BEF
3PEW
P20449 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
FLQ
2FDC
P56981 516.6 Da LogP 4.09 TPSA 134.2 1 viol. ✓ Clean CC(=O)NCCCCCCNC(=O)c1ccc2c(c1)C3(c4ccc(cc4Oc5c3…
FLU
2NMV
P37954 332.3 Da LogP 3.97 TPSA 87.7 ✓ Ro5 ✓ Clean c1ccc(c(c1)C2=C3C=CC(=O)C=C3Oc4c2ccc(c4)O)C(=O)O
IHP
3RRN
P20449 660.0 Da LogP -3.13 TPSA 400.6 3 viol. ✓ Clean C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O…
M2A
5ELX
P20449 560.4 Da LogP 0.16 TPSA 250.7 3 viol. ✓ Clean CNc1ccccc1C(=O)O[C@@H]2[C@@H]([C@@H](O[C@H]2n3c…
MLI
5ZBZ
P60842 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
SAU
5ZBZ
P60842 332.3 Da LogP 3.43 TPSA 40.8 ✓ Ro5 ✓ Clean C[n+]1cc2c(ccc3c2OCO3)c4c1c5cc6c(cc5cc4)OCO6

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.