Protein profile

PA3821

preprotein translocase subunit SecD

Genome: NC_002516.2

Gene: PA3821 secD Structure source: AlphaFold UniProt Q9HXI1
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Amino acids 620
Annotations 7
Features 42
PDB binders 2
Druggability 0.884

Overview

Basic information about this protein and its source genome.

Accession
PA3821
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3821 secD
Status
annotated
Amino acids
620
Structure source
AlphaFold
GO
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:0015450 Primary active carrier-mediated transport of a protein across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated. GO:0065002 The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore. GO:0006605 The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif. GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0043952 The process in which unfolded proteins are transported across the cytoplasmic membrane in Gram-positive and Gram-negative bacteria by the Sec complex, in a process involving proteolytic cleavage of an N-terminal signal peptide.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
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 0.884
Structure –
Pocket –

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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0015450 Primary active carrier-mediated transport of a protein across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated.
  • GO:0065002 The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore.
  • GO:0006605 The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
  • GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0043952 The process in which unfolded proteins are transported across the cytoplasmic membrane in Gram-positive and Gram-negative bacteria by the Sec complex, in a process involving proteolytic cleavage of an N-terminal signal peptide.
  • GO:0006886 The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.

Sequence Features

Domain/signature hits from InterPro and related databases.

42 records
Show feature table
Start End DB Term Name
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
443 606 Pfam PF02355 Protein export membrane protein
443 606 InterPro IPR022813 Protein-export membrane protein SecD/SecF, archaeal and bacterial
117 141 Pfam PF07549 SecD/SecF GG Motif
117 141 InterPro IPR022646 Protein-export membrane protein SecD/SecF/SecDF, conserved site
2 104 Pfam PF13721 SecD export protein N-terminal TM region
2 104 InterPro IPR027398 SecD export protein N-terminal TM domain
1 24 Phobius SIGNAL_PEPTIDE Signal peptide region
554 575 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
224 440 Gene3D G3DSA:3.30.70.3400 -
224 284 FunFam G3DSA:3.30.70.3400:FF:000003 Preprotein translocase subunit SecD
482 487 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
587 610 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
3 619 Hamap MF_01463_B Protein translocase subunit SecD [secD].
3 619 InterPro IPR005791 Protein translocase subunit SecD
281 437 Gene3D G3DSA:3.30.1360.200 -
488 506 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
589 611 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
534 553 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
325 611 SUPERFAMILY SSF82866 Multidrug efflux transporter AcrB transmembrane domain
554 576 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
434 616 FunFam G3DSA:1.20.1640.10:FF:000004 Protein translocase subunit SecD
611 620 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
20 24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
507 511 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 10 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
279 437 FunFam G3DSA:3.30.1360.200:FF:000001 Protein translocase subunit SecD
462 481 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
511 533 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
576 586 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
441 613 Gene3D G3DSA:1.20.1640.10 Multidrug efflux transporter AcrB transmembrane domain
343 599 NCBIfam TIGR00916 SecD/SecF family protein translocase subunit
343 599 InterPro IPR022645 Protein-export membrane protein SecD/SecF, bacterial
512 533 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
4 610 PANTHER PTHR30081 PROTEIN-EXPORT MEMBRANE PROTEIN SEC
4 610 InterPro IPR022813 Protein-export membrane protein SecD/SecF, archaeal and bacterial
488 507 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
124 606 NCBIfam TIGR01129 protein translocase subunit SecD
124 606 InterPro IPR005791 Protein translocase subunit SecD
462 481 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
25 461 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
11 19 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.

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

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA3821
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 0.884

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.

52 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
15P
5XAN
Q9RTE3 1529.8 Da LogP 0.17 TPSA 334.1 2 viol. ✓ Clean COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO…
OLC
5YHF
Q5SKE6 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)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.