Protein profile

KP13_02053

Protein-export membrane protein secD

Genome: KpKP13

Gene: AHE46056.1 secD Structure source: AlphaFold + ColabFold UniProt A0A0H3GNZ4
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Amino acids 615
Annotations 6
Features 42
PDB binders 2
Druggability 0.962

Overview

Basic information about this protein and its source genome.

Accession
KP13_02053
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46056.1 secD
Status
annotated
Amino acids
615
Structure source
AlphaFold + ColabFold
GO
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. 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. 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: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
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
93.333
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
86.91

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 0.962
Structure A0A0H3GNZ4
Pocket Pocket 50
P2Rank 0.589
Structure A0A0H3GNZ4
Pocket Pocket 1
ColabFold model
FPocket 0.994 · Pocket 39
P2Rank 0.594 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 156 / 4744 genomes with a hit
Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • 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.
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • 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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

42 records
Show feature table
Start End DB Term Name
498 502 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
278 431 FunFam G3DSA:3.30.1360.200:FF:000001 Protein translocase subunit SecD
548 570 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
580 602 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
577 605 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
278 431 Gene3D G3DSA:3.30.1360.200 -
525 544 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
410 606 SUPERFAMILY SSF82866 Multidrug efflux transporter AcrB transmembrane domain
452 470 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
473 476 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
7 25 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
123 196 Gene3D G3DSA:3.30.70.3400 -
433 601 Pfam PF02355 Protein export membrane protein
433 601 InterPro IPR022813 Protein-export membrane protein SecD/SecF, archaeal and bacterial
606 615 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
545 571 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
428 611 FunFam G3DSA:1.20.1640.10:FF:000004 Protein translocase subunit SecD
453 472 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
3 615 Hamap MF_01463_B Protein translocase subunit SecD [secD].
3 615 InterPro IPR005791 Protein translocase subunit SecD
26 452 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
221 433 Gene3D G3DSA:3.30.70.3400 -
475 497 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
123 601 NCBIfam TIGR01129 protein translocase subunit SecD
123 601 InterPro IPR005791 Protein translocase subunit SecD
434 612 Gene3D G3DSA:1.20.1640.10 Multidrug efflux transporter AcrB transmembrane domain
1 6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
2 103 Pfam PF13721 SecD export protein N-terminal TM region
2 103 InterPro IPR027398 SecD export protein N-terminal TM domain
477 497 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
502 524 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
5 607 PANTHER PTHR30081 PROTEIN-EXPORT MEMBRANE PROTEIN SEC
5 607 InterPro IPR022813 Protein-export membrane protein SecD/SecF, archaeal and bacterial
503 524 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
221 279 FunFam G3DSA:3.30.70.3400:FF:000001 Protein translocase subunit SecD
572 576 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
120 140 Pfam PF07549 SecD/SecF GG Motif
120 140 InterPro IPR022646 Protein-export membrane protein SecD/SecF/SecDF, conserved site
31 105 Gene3D G3DSA:3.30.70.260 -
345 594 NCBIfam TIGR00916 SecD/SecF family protein translocase subunit
345 594 InterPro IPR022645 Protein-export membrane protein SecD/SecF, bacterial

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_A0A0H3GNZ4
AlphaFold — — full sequence — Viewing
ColabFold KP13_02053
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
50 0.962
2 0.742
46 0.446

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 8.97 0.48
2 4.49 0.191
3 2.76 0.084
4 2.39 0.064
5 2.16 0.051

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.