Protein profile

PA0482

malate synthase G

Genome: NC_002516.2

Gene: PA0482 glcB Structure source: Experimental + AlphaFold UniProt Q9I636
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Amino acids 725
Annotations 8
Features 19
PDB binders 50
Druggability 0.75

Overview

Basic information about this protein and its source genome.

Accession
PA0482
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA0482 glcB
Status
annotated
Amino acids
725
Structure source
Experimental + AlphaFold
EC
2.3.3.9
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0000287 Binding to a magnesium (Mg) ion. GO:0004474 Catalysis of the reaction: acetyl-CoA + glyoxylate + H2O = (S)-malate + CoA + H+. GO:0009436 The chemical reactions and pathways resulting in the breakdown of glyoxylate, the anion of glyoxylic acid, HOC-COOH. GO:0006097 A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate. GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

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 0.75
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MTERVQVGGLQVAKVLFDFVNNEAIPGTGVSADTFWTGAEAVINDLAPKNKALLAKRDELQAKIDGWHQARAGQAHDAVAYKAFLEEIGYLLPEAEDFQAGTQNVDDEIARMAGPQLVVPVMNARFALNASNARWGSLYDALYGTDVISEEGGAEKGKGYNKVRGDKVIAFARAFLDEAAPLESGSHVDATSYSVKNGALVVALKNGSETGLKNAGQFLAFQGDAAKPQAVLLKHNGLHFEIQIDPSSPVGQTDAAGVKDVLMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDLAEEVSKGGSTFTRTMNPDRVYTRADGSELTLHGRSLLFVRNVGHLMTNDAILDKDGNEVPEGIQDGLFTSLIAIHDLNGNTSRKNSRTGSVYIVKPKMHGPEEAAFTNELFGRVEDVLGLPRNTLKVGIMDEERRTTVNLKACIKAAKDRVVFINTGFLDRTGDEIHTSMEAGAVVRKGAMKSEKWIGAYENNNVDVGLATGLQGKAQIGKGMWAMPDLMAAMLEQKIGHPLAGANTAWVPSPTAATLHALHYHKVDVFARQAELAKRTPASVDDILTIPLAPNTNWTAEEIKNEVDNNAQGILGYVVRWIDQGVGCSKVPDINDVGLMEDRATLRISSQLLANWLRHGVISQEQVVESLKRMAVVVDRQNASDPSYRPMAPNFDDNVAFQAALELVVEGTRQPNGYTEPVLHRRRREFKAKNGL

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0004474 Catalysis of the reaction: acetyl-CoA + glyoxylate + H2O = (S)-malate + CoA + H+.
  • GO:0009436 The chemical reactions and pathways resulting in the breakdown of glyoxylate, the anion of glyoxylic acid, HOC-COOH.
  • GO:0006097 A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
  • GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
18 697 Pfam PF01274 Malate synthase
18 697 InterPro IPR001465 Malate synthase
585 724 Gene3D G3DSA:1.20.1220.12 Malate synthase, domain III
585 724 InterPro IPR044856 Malate synthase, C-terminal superfamily
9 720 CDD cd00728 malate_synt_G
9 720 InterPro IPR006253 Malate synthase G
200 584 FunFam G3DSA:3.20.20.360:FF:000002 Malate synthase G
4 723 NCBIfam TIGR01345 malate synthase G
4 723 InterPro IPR006253 Malate synthase G
249 584 Gene3D G3DSA:3.20.20.360 Malate synthase, domain 3
249 584 InterPro IPR046363 Malate synthase, N-terminal and TIM-barrel domains
2 723 SUPERFAMILY SSF51645 Malate synthase G
2 723 InterPro IPR011076 Malate synthase superfamily
1 237 Gene3D G3DSA:3.20.20.360 Malate synthase, domain 3
1 237 InterPro IPR046363 Malate synthase, N-terminal and TIM-barrel domains
1 722 PANTHER PTHR42739 MALATE SYNTHASE G
1 722 InterPro IPR006253 Malate synthase G
1 725 Hamap MF_00641 Malate synthase G [glcB].
1 725 InterPro IPR006253 Malate synthase G

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

2 + 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 5VFB
X-ray 1.36 Å A,B
100.0% 1-725
PDBe RCSB PDBj File
Viewing
PDB 5OAS
X-ray 1.62 Å A
100.0% 1-725
PDBe RCSB PDBj File
Loaded
AlphaFold PA0482
AlphaFold — — 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 0.75
5 0.323

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 28.43 0.925
2 12.12 0.64
3 10.69 0.574
4 3.18 0.108
5 2.82 0.088

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.

100 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
GOA
5VFB 1.36 Å Open crystal
76.1 Da LogP -0.94 TPSA 57.5 ✓ Ro5 ✓ Clean C(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.