Protein profile

VK055_2542

citrate-sodium symporter

Genome: KpATCC43816

Gene: citS AIK81139.1 Structure source: Experimental + ColabFold UniProt P31602
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Amino acids 446
Annotations 8
Features 45
PDB binders 2
Druggability 0.987

Overview

Basic information about this protein and its source genome.

Accession
VK055_2542
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
citS AIK81139.1
Status
annotated
Amino acids
446
Structure source
Experimental + ColabFold
GO
GO:0008514 OBSOLETE. Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0015711 The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. 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:0046872 Binding to a metal ion. GO:0015293 Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
90.9

Selected Druggability evidence

PDB experimental structure

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 0.987
Structure 9LSJ
Pocket Pocket 3
P2Rank 0.743
Structure 9LSK
Pocket Pocket 1
ColabFold model
FPocket 0.357 · Pocket 4
P2Rank 0.626 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 35 / 4744 genomes with a hit
Normalized 0.007

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:0008514 OBSOLETE. Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0015711 The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage.
  • 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:0046872 Binding to a metal ion.
  • GO:0015293 Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy.
  • GO:0006101 The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboxylate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle.
  • GO:0006814 The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

45 records
Show feature table
Start End DB Term Name
425 444 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
446 446 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
176 198 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
385 424 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
269 286 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
144 168 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
336 358 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
114 132 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
208 230 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
46 66 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
23 440 Pfam PF03390 2-hydroxycarboxylate transporter family
23 440 InterPro IPR004679 2-hydroxycarboxylate transporter
3 446 PIRSF PIRSF005348 YxkH
3 446 InterPro IPR004679 2-hydroxycarboxylate transporter
174 196 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
96 114 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
352 362 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
78 95 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
133 143 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
18 441 NCBIfam TIGR00783 citrate:cation symporter
18 441 InterPro IPR018025 2-hydroxycarboxylate transporter, proteobacteria/firmicutes
115 132 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
23 45 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
79 101 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
208 230 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
2 445 PANTHER PTHR40033 NA(+)-MALATE SYMPORTER
2 445 InterPro IPR004679 2-hydroxycarboxylate transporter
197 207 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
296 315 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
363 384 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
52 69 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
312 330 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
425 445 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
67 77 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
231 267 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
21 40 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
293 311 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
363 385 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
268 286 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
41 45 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
287 292 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
147 169 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
169 173 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
331 351 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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

6 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 5XAS
X-ray 3.47 Å A,B
97.3% 13-446
PDBe RCSB PDBj File
Viewing
PDB 5XAR
X-ray 3.62 Å A,B,C,D
97.3% 13-446
PDBe RCSB PDBj File
Loaded
PDB 5XAT
X-ray 3.76 Å A,B,C,D
97.3% 13-446
PDBe RCSB PDBj File
Loaded
PDB 5X9R
X-ray 3.98 Å A,B
97.3% 13-446
PDBe RCSB PDBj File
Loaded
PDB 9LSJ
X-ray 20.00 Å - —
PDBe RCSB PDBj File
Loaded
PDB 9LSK
X-ray 20.00 Å - —
PDBe RCSB PDBj File
Loaded
ColabFold VK055_2542
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
1 0.922
6 0.509
45 0.27
4 0.231

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 42.57 0.968
2 14.87 0.737
3 10.9 0.585
4 9.98 0.537
5 8.03 0.427

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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
BOG
5XAR 3.62 Å Open crystal
292.4 Da LogP 0.16 TPSA 99.4 ✓ Ro5 ✓ Clean CCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)…
FLC
5X9R 3.98 Å Open crystal
189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])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.