Protein profile

VK055_3079

malate synthase A

Genome: KpATCC43816

Gene: aceB AIK81664.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLT0
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Amino acids 533
Annotations 3
Features 20
PDB binders 1
Druggability 0.522

Overview

Basic information about this protein and its source genome.

Accession
VK055_3079
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
aceB AIK81664.1
Status
annotated
Amino acids
533
Structure source
AlphaFold + ColabFold
GO
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: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. GO:0004474 Catalysis of the reaction: acetyl-CoA + glyoxylate + H2O = (S)-malate + CoA + H+.

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 (%)
21.767
Localization
Cytoplasmic
ColabFold pLDDT
96.86

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 0.522
Structure A0A0H3GLT0
Pocket Pocket 2
P2Rank 0.954
Structure A0A0H3GLT0
Pocket Pocket 1
ColabFold model
FPocket 0.903 · Pocket 2
P2Rank 0.833 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 161 / 4744 genomes with a hit
Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • 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: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.
  • GO:0004474 Catalysis of the reaction: acetyl-CoA + glyoxylate + H2O = (S)-malate + CoA + H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
11 532 SUPERFAMILY SSF51645 Malate synthase G
11 532 InterPro IPR011076 Malate synthase superfamily
24 532 NCBIfam TIGR01344 malate synthase A
24 532 InterPro IPR006252 Malate synthase A
412 533 FunFam G3DSA:1.20.1220.12:FF:000001 Malate synthase
2 533 PIRSF PIRSF001363 Malate_synth
2 533 InterPro IPR006252 Malate synthase A
412 533 Gene3D G3DSA:1.20.1220.12 Malate synthase, domain III
412 533 InterPro IPR044856 Malate synthase, C-terminal superfamily
12 532 Pfam PF01274 Malate synthase
12 532 InterPro IPR001465 Malate synthase
2 411 Gene3D G3DSA:3.20.20.360 Malate synthase, domain 3
2 411 InterPro IPR046363 Malate synthase, N-terminal and TIM-barrel domains
24 533 CDD cd00727 malate_synt_A
24 533 InterPro IPR006252 Malate synthase A
266 281 ProSitePatterns PS00510 Malate synthase signature.
266 281 InterPro IPR019830 Malate synthase, conserved site
8 530 PANTHER PTHR42902 MALATE SYNTHASE
8 530 InterPro IPR006252 Malate synthase A
7 411 FunFam G3DSA:3.20.20.360:FF:000001 Malate synthase

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_A0A0H3GLT0
AlphaFold — — full sequence — Viewing
ColabFold VK055_3079
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
2 0.522
1 0.235
13 0.17
20 0.125

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 43.26 0.954
2 5.13 0.194
3 3.48 0.101
4 3.43 0.098
5 3.19 0.087

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.

1 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
OXL
3CV2
P08997 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=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.