Protein profile

VK055_1571

ATP-dependent Clp protease ATP-binding subunit ClpA

Genome: KpATCC43816

Gene: AIK80191.1 clpA Structure source: AlphaFold + ColabFold UniProt A0A0H3GQX4
Amino acids 759
Annotations 7
Features 55
PDB binders 7
Druggability 0.461

Overview

Basic information about this protein and its source genome.

Accession
VK055_1571
Gene
AIK80191.1 clpA
Status
annotated
Amino acids
759
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
41.714
Human E-value
6.09e-38
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
63.228
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
83.44

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 0.461
Structure A0A0H3GQX4
Pocket Pocket 1
P2Rank 0.66
Structure A0A0H3GQX4
Pocket Pocket 1
ColabFold model
FPocket 0.16 · Pocket 56
P2Rank 0.665 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 222 / 4744 genomes with a hit
Normalized 0.047

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0043335 The process of assisting in the disassembly of non-covalent linkages in a protein or protein aggregate, often where the proteins are in a non-functional or denatured state.
  • 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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0008233 Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
  • GO:0034605 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Sequence Features

Domain/signature hits from InterPro and related databases.

55 records
Show feature table
Start End DB Term Name
1 145 ProSiteProfiles PS51903 Clp repeat (R) domain profile.
1 145 InterPro IPR004176 Clp, repeat (R) domain
450 651 CDD cd19499 RecA-like_ClpB_Hsp104-like
352 439 FunFam G3DSA:1.10.8.60:FF:000011 ATP-dependent Clp protease ATP-binding subunit
654 734 Pfam PF10431 C-terminal, D2-small domain, of ClpB protein
654 734 InterPro IPR019489 Clp ATPase, C-terminal
158 351 Gene3D G3DSA:3.40.50.300 -
158 351 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
190 345 CDD cd00009 AAA
212 343 Pfam PF00004 ATPase family associated with various cellular activities (AAA)
212 343 InterPro IPR003959 ATPase, AAA-type, core
8 743 PANTHER PTHR11638 ATP-DEPENDENT CLP PROTEASE
207 352 SMART SM00382 AAA_5
207 352 InterPro IPR003593 AAA+ ATPase domain
488 655 SMART SM00382 AAA_5
488 655 InterPro IPR003593 AAA+ ATPase domain
170 427 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
170 427 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
519 537 ProSitePatterns PS00871 Chaperonins clpA/B signature 2.
519 537 InterPro IPR028299 ClpA/B, conserved site 2
13 62 Pfam PF02861 Clp amino terminal domain, pathogenicity island component
13 62 InterPro IPR004176 Clp, repeat (R) domain
440 653 Gene3D G3DSA:3.40.50.300 -
440 653 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
563 581 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature
563 581 InterPro IPR001270 ClpA/B family
534 552 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature
534 552 InterPro IPR001270 ClpA/B family
492 510 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature
492 510 InterPro IPR001270 ClpA/B family
596 610 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature
596 610 InterPro IPR001270 ClpA/B family
654 743 SMART SM01086 ClpB_D2_small_2
654 743 InterPro IPR019489 Clp ATPase, C-terminal
351 453 Pfam PF17871 AAA lid domain
351 453 InterPro IPR041546 ClpA/ClpB, AAA lid domain
440 653 FunFam G3DSA:3.40.50.300:FF:000268 ATP-dependent Clp protease, ATP-binding subunit ClpA
303 315 ProSitePatterns PS00870 Chaperonins clpA/B signature 1.
303 315 InterPro IPR018368 ClpA/B, conserved site 1
157 351 FunFam G3DSA:3.40.50.300:FF:000271 ATP-dependent Clp protease ATP-binding subunit ClpA
142 161 MobiDBLite mobidb-lite consensus disorder prediction
487 648 Pfam PF07724 AAA domain (Cdc48 subfamily)
487 648 InterPro IPR003959 ATPase, AAA-type, core
1 141 SUPERFAMILY SSF81923 Double Clp-N motif
1 141 InterPro IPR036628 Clp, N-terminal domain superfamily
3 735 NCBIfam TIGR02639 ATP-dependent Clp protease ATP-binding subunit ClpA
3 735 InterPro IPR013461 ATP-dependent Clp protease ATP-binding subunit ClpA
654 759 Gene3D G3DSA:1.10.8.60 -
140 173 MobiDBLite mobidb-lite consensus disorder prediction
1 143 Gene3D G3DSA:1.10.1780.10 -
1 143 InterPro IPR036628 Clp, N-terminal domain superfamily
352 439 Gene3D G3DSA:1.10.8.60 -
438 749 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
438 749 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 143 FunFam G3DSA:1.10.1780.10:FF:000002 ATP-dependent Clp protease ATP-binding subunit ClpA

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_A0A0H3GQX4
AlphaFold full sequence Viewing
ColabFold VK055_1571
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
10 0.022
4 0.002
31 0.0
57 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 15.01 0.66
2 11.55 0.532
3 4.41 0.153
4 3.94 0.126
5 2.6 0.061

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
ACP Q9RA63 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AGS P0ABH9 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)…
ANP Q9RA63 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)…
MNT Q9RA63 544.4 Da LogP 1.19 TPSA 230.5 2 viol. ✓ Clean CNc1ccccc1C(=O)O[C@H]2C[C@@H](O[C@@H]2CO[P@](=O…
RPI P37571 254.2 Da LogP -1.61 TPSA 168.8 1 viol. ✓ Clean [H]/N=C(/NCCC[C@@H](C(=O)O)N)\NP(=O)(O)O
SRT P37571 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@H](C(=O)O)O)(C(=O)O)O
Y1 P0ABH9 88.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Y+2]

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.