Protein profile

PA3002

transcription-repair coupling factor

Genome: NC_002516.2

Gene: PA3002 mfd Structure source: AlphaFold UniProt Q9HZK3
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Amino acids 1148
Annotations 13
Features 53
PDB binders 3
Druggability 0.781

Overview

Basic information about this protein and its source genome.

Accession
PA3002
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3002 mfd
Status
annotated
Amino acids
1148
Structure source
AlphaFold
EC
3.6.4.-
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0003684 Binding to damaged DNA. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0015616 Generation of movement along a single- or double-stranded DNA molecule, driven by ATP hydrolysis. GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.534
Human E-value
1.07e-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 0.781
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

12
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003684 Binding to damaged DNA.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0015616 Generation of movement along a single- or double-stranded DNA molecule, driven by ATP hydrolysis.
  • GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0043175 Binding to an RNA polymerase core enzyme, containing a specific subunit composition defined as the core enzyme.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0000716 The identification of lesions on the actively transcribed strand of the DNA duplex as well as a small subset of lesions not recognized by the general nucleotide-excision repair pathway.
  • 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.
  • GO:0003676 Binding to a nucleic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

53 records
Show feature table
Start End DB Term Name
23 334 Gene3D G3DSA:3.40.50.11180 -
992 1144 SUPERFAMILY SSF143517 TRCF domain-like
992 1144 InterPro IPR037235 TRCF-like, C-terminal D7 domain
477 574 SMART SM01058 CarD_TRCF_2
477 574 InterPro IPR003711 CarD-like/TRCF, RNAP-interacting domain
478 573 Pfam PF02559 CarD-like/TRCF domain
478 573 InterPro IPR003711 CarD-like/TRCF, RNAP-interacting domain
778 988 FunFam G3DSA:3.40.50.300:FF:000300 Transcription-repair-coupling factor
476 987 Gene3D G3DSA:3.40.50.300 -
476 987 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
351 464 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
351 464 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
128 217 Pfam PF17757 UvrB interaction domain
128 217 InterPro IPR041471 UvrB, interaction domain
598 788 SMART SM00487 ultradead3
598 788 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
568 973 PANTHER PTHR47964 ATP-DEPENDENT DNA HELICASE HOMOLOG RECG, CHLOROPLASTIC
568 973 InterPro IPR047112 ATP-dependent DNA helicase RecG/Transcription-repair-coupling factor
824 908 SMART SM00490 helicmild6
824 908 InterPro IPR001650 Helicase, C-terminal
355 451 Gene3D G3DSA:3.40.50.11140 -
1006 1106 SMART SM00982 TRCF_a_2_a
1006 1106 InterPro IPR005118 Transcription-repair-coupling factor, C-terminal domain
148 1079 NCBIfam TIGR00580 transcription-repair coupling factor
148 1079 InterPro IPR004576 Transcription-repair coupling factor
10 340 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
10 340 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
469 546 SUPERFAMILY SSF141259 CarD-like
469 546 InterPro IPR036101 CarD-like/TRCF, RNAP-interacting domain superfamily
522 781 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
522 781 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
603 763 Pfam PF00270 DEAD/DEAH box helicase
603 763 InterPro IPR011545 DEAD/DEAH box helicase domain
798 952 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile.
798 952 InterPro IPR001650 Helicase, C-terminal
540 779 Gene3D G3DSA:3.40.50.300 -
540 779 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
587 779 CDD cd17991 DEXHc_TRCF
1003 1147 Gene3D G3DSA:3.90.1150.50 -
1003 1147 InterPro IPR037235 TRCF-like, C-terminal D7 domain
1007 1098 Pfam PF03461 TRCF domain
1007 1098 InterPro IPR005118 Transcription-repair-coupling factor, C-terminal domain
804 907 Pfam PF00271 Helicase conserved C-terminal domain
804 907 InterPro IPR001650 Helicase, C-terminal
616 777 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
616 777 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
34 1104 Hamap MF_00969 Transcription-repair-coupling factor [mfd].
34 1104 InterPro IPR004576 Transcription-repair coupling factor
128 213 Gene3D G3DSA:3.30.2060.10 -
540 777 FunFam G3DSA:3.40.50.300:FF:000546 Transcription-repair-coupling factor
780 988 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
780 988 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
481 539 Gene3D G3DSA:2.40.10.170 -

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 PA3002
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
1 0.529

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.

53 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
AGS
6M6B
Q72KB4 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
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

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.