Protein profile

VK055_5102

lipid A export permease/ATP-binding protein MsbA

Genome: KpATCC43816

Gene: iroC AIK83628.1 Structure source: AlphaFold + ColabFold UniProt A4GZE9
Amino acids 1195
Annotations 8
Features 78
PDB binders 6
Druggability 0.934

Overview

Basic information about this protein and its source genome.

Accession
VK055_5102
Gene
iroC AIK83628.1
Status
annotated
Amino acids
1195
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
46.667
Human E-value
1.44e-13
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
45.238
Localization
CytoplasmicMembrane
ColabFold pLDDT
87.99

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 0.934
Structure A4GZE9
Pocket Pocket 83
P2Rank 0.888
Structure A4GZE9
Pocket Pocket 1
ColabFold model
FPocket 0.689 · Pocket 82
P2Rank 0.889 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 7 / 4744 genomes with a hit
Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0140359 Primary active transporter characterized by two nucleotide-binding domains and two transmembrane domains. Uses the energy generated from ATP hydrolysis to drive the transport of a substance across a membrane.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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:0015421 Catalysis of the reaction: ATP + H2O + oligopeptide(out) = ADP + phosphate + oligopeptide(in).

Sequence Features

Domain/signature hits from InterPro and related databases.

78 records
Show feature table
Start End DB Term Name
625 651 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
663 685 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
49 551 PANTHER PTHR24221 ATP-BINDING CASSETTE SUB-FAMILY B
49 551 InterPro IPR039421 Type 1 protein exporter
630 899 Pfam PF00664 ABC transporter transmembrane region
630 899 InterPro IPR011527 ABC transporter type 1, transmembrane domain
10 277 Pfam PF00664 ABC transporter transmembrane region
10 277 InterPro IPR011527 ABC transporter type 1, transmembrane domain
26 44 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
7 25 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
224 246 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
630 911 ProSiteProfiles PS50929 ABC transporter integral membrane type-1 fused domain profile.
630 911 InterPro IPR011527 ABC transporter type 1, transmembrane domain
943 1180 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
943 1180 InterPro IPR003439 ABC transporter-like, ATP-binding domain
316 564 FunFam G3DSA:3.40.50.300:FF:000299 ABC transporter ATP-binding protein/permease
264 287 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
663 684 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 33 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
119 141 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
652 662 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
848 870 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
849 872 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
253 263 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
229 252 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
166 228 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
629 919 CDD cd18546 ABC_6TM_Rv0194_D2_like
66 117 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
969 1151 SMART SM00382 AAA_5
969 1151 InterPro IPR003593 AAA+ ATPase domain
347 564 SMART SM00382 AAA_5
347 564 InterPro IPR003593 AAA+ ATPase domain
935 1189 Gene3D G3DSA:3.40.50.300 -
935 1189 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
463 477 ProSitePatterns PS00211 ABC transporters family signature.
463 477 InterPro IPR017871 ABC transporter-like, conserved site
960 1109 Pfam PF00005 ABC transporter
960 1109 InterPro IPR003439 ABC transporter-like, ATP-binding domain
142 146 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
45 65 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
612 926 Gene3D G3DSA:1.20.1560.10 ABC transporter type 1, transmembrane domain
612 926 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily
937 1179 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
937 1179 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
322 561 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
322 561 InterPro IPR003439 ABC transporter-like, ATP-binding domain
43 65 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
338 491 Pfam PF00005 ABC transporter
338 491 InterPro IPR003439 ABC transporter-like, ATP-binding domain
318 559 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
318 559 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
261 283 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
288 624 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
118 141 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
626 648 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
769 786 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
744 763 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
147 165 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
9 28 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
146 163 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
616 933 SUPERFAMILY SSF90123 ABC transporter transmembrane region
616 933 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily
941 1183 FunFam G3DSA:3.40.50.300:FF:000836 ABC transporter B family member 25
787 848 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
767 786 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
685 743 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 314 Gene3D G3DSA:1.20.1560.10 ABC transporter type 1, transmembrane domain
1 314 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily
764 768 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
317 564 Gene3D G3DSA:3.40.50.300 -
317 564 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
10 290 ProSiteProfiles PS50929 ABC transporter integral membrane type-1 fused domain profile.
10 290 InterPro IPR011527 ABC transporter type 1, transmembrane domain
873 1195 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
735 757 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
3 303 SUPERFAMILY SSF90123 ABC transporter transmembrane region
3 303 InterPro IPR036640 ABC transporter type 1, transmembrane 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.

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_A4GZE9
AlphaFold full sequence Viewing
ColabFold VK055_5102
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
83 0.934
54 0.631

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 18.52 0.824
2 11.38 0.608
3 7.96 0.423
4 3.25 0.113
5 3.07 0.102

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.

59 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
0JZ P21447 687.4 Da LogP 1.74 TPSA 126.0 1 viol. ✓ Clean CC(C)[C@@H]1c2nc(c[se]2)C(=O)N[C@@H](c3nc(c[se]…
2J8 P21447 687.4 Da LogP 1.74 TPSA 126.0 1 viol. ✓ Clean CC(C)[C@H]1c2nc(c[se]2)C(=O)N[C@H](c3nc(c[se]3)…
4C8 P21447 564.7 Da LogP 7.29 TPSA 9.2 2 viol. ✓ Clean c1cc(c(cc1Br)Br)Oc2c(cc(cc2Br)Br)Br
AGS Q9WYC4 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 Q99T13 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)…
CLR P21439-2 386.7 Da LogP 7.39 TPSA 20.2 1 viol. ✓ Clean CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3…

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.