Protein profile

PA0105

cytochrome C oxidase subunit II

Genome: NC_002516.2

Gene: PA0105 coxB Structure source: AlphaFold UniProt Q9I727
Amino acids 374
Annotations 11
Features 51
PDB binders 28
Druggability 0.709

Overview

Basic information about this protein and its source genome.

Accession
PA0105
Gene
PA0105 coxB
Status
annotated
Amino acids
374
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
37.278
Human E-value
5.29e-38
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
CytoplasmicMembrane

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 0.709
Structure
Pocket

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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0098803 Any protein complex that is part of a respiratory chain.
  • GO:0005507 Binding to a copper (Cu) ion.
  • GO:0004129 Catalysis of the reaction: 4 Fe(II)-[cytochrome c] + O2 + 8 H+(in) = 4 Fe(III)-[cytochrome c] + 2 H2O + 4 H+(out).
  • GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0042773 The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP.
  • GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0022900 A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors.

Sequence Features

Domain/signature hits from InterPro and related databases.

51 records
Show feature table
Start End DB Term Name
121 240 Pfam PF00116 Cytochrome C oxidase subunit II, periplasmic domain
121 240 InterPro IPR002429 Cytochrome c oxidase subunit II-like C-terminal
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
274 348 Pfam PF13442 Cytochrome C oxidase, cbb3-type, subunit III
274 348 InterPro IPR009056 Cytochrome c-like domain
224 241 PRINTS PR01166 Cytochrome c oxidase subunit II signature
206 223 PRINTS PR01166 Cytochrome c oxidase subunit II signature
186 206 PRINTS PR01166 Cytochrome c oxidase subunit II signature
115 134 PRINTS PR01166 Cytochrome c oxidase subunit II signature
81 93 PRINTS PR01166 Cytochrome c oxidase subunit II signature
162 183 PRINTS PR01166 Cytochrome c oxidase subunit II signature
93 113 PRINTS PR01166 Cytochrome c oxidase subunit II signature
37 113 Gene3D G3DSA:1.10.287.90 -
37 113 InterPro IPR036257 Cytochrome C oxidase subunit II, transmembrane domain superfamily
187 235 ProSitePatterns PS00078 CO II and nitrous oxide reductase dinuclear copper centers signature.
187 235 InterPro IPR001505 Copper centre Cu(A)
1 22 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
67 86 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
20 115 ProSiteProfiles PS50999 Cytochrome oxidase subunit II transmembrane region profile.
20 115 InterPro IPR011759 Cytochrome C oxidase subunit II, transmembrane domain
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
254 374 Gene3D G3DSA:1.10.760.10 -
254 374 InterPro IPR036909 Cytochrome c-like domain superfamily
46 66 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
87 105 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
87 109 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
273 353 ProSiteProfiles PS51007 Cytochrome c family profile.
273 353 InterPro IPR009056 Cytochrome c-like domain
37 113 FunFam G3DSA:1.10.287.90:FF:000009 Cytochrome c oxidase subunit 2
44 66 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
12 112 SUPERFAMILY SSF81464 Cytochrome c oxidase subunit II-like, transmembrane region
12 112 InterPro IPR036257 Cytochrome C oxidase subunit II, transmembrane domain superfamily
114 252 Gene3D G3DSA:2.60.40.420 -
114 252 InterPro IPR008972 Cupredoxin
9 259 PANTHER PTHR22888 CYTOCHROME C OXIDASE, SUBUNIT II
9 259 InterPro IPR045187 Cytochrome c/quinol oxidase subunit II
23 104 Pfam PF02790 Cytochrome C oxidase subunit II, transmembrane domain
23 104 InterPro IPR011759 Cytochrome C oxidase subunit II, transmembrane domain
106 374 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
116 253 ProSiteProfiles PS50857 Cytochrome oxidase subunit II copper A binding domain profile.
116 253 InterPro IPR002429 Cytochrome c oxidase subunit II-like C-terminal
23 45 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
18 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
32 251 NCBIfam TIGR02866 cytochrome c oxidase subunit II
32 251 InterPro IPR014222 Cytochrome c oxidase, subunit II
116 257 SUPERFAMILY SSF49503 Cupredoxins
116 257 InterPro IPR008972 Cupredoxin
7 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
221 358 SUPERFAMILY SSF46626 Cytochrome c
221 358 InterPro IPR036909 Cytochrome c-like domain superfamily

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 PA0105
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 0.709

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.

78 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
3PE Q03736 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
4AG Q5SLI2 568.9 Da LogP 10.40 TPSA 72.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@@H](CO)OC(=O)CCCCCCCCC…
5PL Q5SLI2 1233.7 Da LogP 15.13 TPSA 245.7 4 viol. ✓ Clean CCCCCCCCCCCCCCCCCCCNC(=O)[C@@H](CO[C@@H]1[C@@H]…
6PH P00410 592.8 Da LogP 8.95 TPSA 119.4 2 viol. ✓ Clean CCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCCCC)C…
7E8 Q5SLI2 300.4 Da LogP 3.36 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCC/C=C\CCCCCC(=O)OC[C@@H](CO)O
7E9 Q5SLI2 300.4 Da LogP 3.36 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCC/C=C\CCCCCC(=O)OC(CO)CO
7PH P00410 564.7 Da LogP 8.17 TPSA 119.4 2 viol. ✓ Clean CCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCCC)COP…
8PE P00410 692.0 Da LogP 10.50 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC…
9PE P00410 593.8 Da LogP 7.77 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCC)CO[P…
CDL P00410 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
CN3 P00410 834.9 Da LogP 7.02 TPSA 236.9 3 viol. ✓ Clean CCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](C…
CN5 P00410 634.6 Da LogP 5.59 TPSA 184.3 3 viol. ✓ Clean CCCCCCCCCCCCCCC(=O)OCCCO[P@](=O)(O)OC[C@H](CO[P…
CUA P00410 127.1 Da LogP -0.01 TPSA 0.0 ✓ Ro5 ✓ Clean [Cu][Cu]
DMU Q3J5G0 482.6 Da LogP -1.23 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)C…
DXC Q03736 392.6 Da LogP 4.48 TPSA 77.8 ✓ Ro5 ✓ Clean C[C@H](CCC(=O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C…
FES P00410 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
HTH Q3J5G0 148.2 Da LogP -0.11 TPSA 60.7 ✓ Ro5 ✓ Clean CCCC[C@H]([C@H](CO)O)O
HTO Q03736 148.2 Da LogP -0.11 TPSA 60.7 ✓ Ro5 ✓ Clean CCCC[C@H]([C@@H](CO)O)O
LDA P08306 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
LMT P08306 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
LMU Q03736 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O…
PCF P00410 734.1 Da LogP 10.61 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)([O-])OCC…
PEF P00410 692.0 Da LogP 10.50 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)…
PEO P08306 34.0 Da LogP 0.02 TPSA 40.5 ✓ Ro5 ✓ Clean OO
PER P08306 32.0 Da LogP -2.38 TPSA 46.1 ✓ Ro5 ✓ Clean [O-][O-]
PTY P00410 734.1 Da LogP 11.67 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC…
TRD Q3J5G0 184.4 Da LogP 5.32 TPSA 0.0 1 viol. ✓ Clean CCCCCCCCCCCCC
UQ6 P00410 592.9 Da LogP 11.56 TPSA 58.9 2 viol. ✓ Clean Cc1c(c(c(c(c1O)OC)OC)O)C\C=C(/C)\CC\C=C(/C)\CC\…

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.