Protein profile

VK055_0962

3-carboxy-cis,cis-muconate cycloisomerase

Genome: KpATCC43816

Gene: AIK79585.1 pcaB Structure source: AlphaFold + ColabFold UniProt A0A0H3GSE2
Export view
Amino acids 444
Annotations 5
Features 28
PDB binders 5
Druggability 0.55

Overview

Basic information about this protein and its source genome.

Accession
VK055_0962
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK79585.1 pcaB
Status
annotated
Amino acids
444
Structure source
AlphaFold + ColabFold
EC
5.5.1.2
GO
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:0019619 The chemical reactions and pathways resulting in the breakdown of 3,4-dihydroxybenzoate. GO:0047472 Catalysis of the reaction: 2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate = 3-carboxy-cis,cis-muconate + H+. GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.736
Human E-value
1.03e-11
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
32.642
Localization
Cytoplasmic
ColabFold pLDDT
96.5

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 0.55
Structure A0A0H3GSE2
Pocket Pocket 1
P2Rank 0.025
Structure A0A0H3GSE2
Pocket Pocket 1
ColabFold model
FPocket 0.828 · Pocket 1
P2Rank 0.075 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 31 / 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.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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:0019619 The chemical reactions and pathways resulting in the breakdown of 3,4-dihydroxybenzoate.
  • GO:0047472 Catalysis of the reaction: 2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate = 3-carboxy-cis,cis-muconate + H+.
  • GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
7 439 PANTHER PTHR43172 ADENYLOSUCCINATE LYASE
355 434 SMART SM00998 ADSL_C_2
355 434 InterPro IPR019468 Adenylosuccinate lyase C-terminal
11 436 CDD cd01597 pCLME
1 351 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain)
354 441 Gene3D G3DSA:1.10.40.30 -
6 339 NCBIfam TIGR02426 3-carboxy-cis,cis-muconate cycloisomerase
6 339 InterPro IPR012789 3-carboxy-cis,cis-muconate cycloisomerase-like
6 440 SUPERFAMILY SSF48557 L-aspartase-like
6 440 InterPro IPR008948 L-Aspartase-like
267 276 ProSitePatterns PS00163 Fumarate lyases signature.
267 276 InterPro IPR020557 Fumarate lyase, conserved site
356 433 Pfam PF10397 Adenylosuccinate lyase C-terminus
356 433 InterPro IPR019468 Adenylosuccinate lyase C-terminal
137 155 PRINTS PR00149 Fumarate lyase superfamily signature
137 155 InterPro IPR000362 Fumarate lyase family
222 249 PRINTS PR00149 Fumarate lyase superfamily signature
222 249 InterPro IPR000362 Fumarate lyase family
267 283 PRINTS PR00149 Fumarate lyase superfamily signature
267 283 InterPro IPR000362 Fumarate lyase family
92 110 PRINTS PR00149 Fumarate lyase superfamily signature
92 110 InterPro IPR000362 Fumarate lyase family
132 152 PRINTS PR00145 Argininosuccinate lyase family signature
267 283 PRINTS PR00145 Argininosuccinate lyase family signature
91 113 PRINTS PR00145 Argininosuccinate lyase family signature
222 246 PRINTS PR00145 Argininosuccinate lyase family signature
5 291 Pfam PF00206 Lyase
5 291 InterPro IPR022761 Fumarate lyase, N-terminal

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

Loading 3D structure...

Legend High Medium Low

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_A0A0H3GSE2
AlphaFold — — full sequence — Viewing
ColabFold VK055_0962
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
4 0.072
9 0.072
2 0.009
28 0.0

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 1.72 0.025
2 1.69 0.024
3 1.32 0.013
4 1.18 0.009
5 1.07 0.006

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.

55 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
DTT
1RE5
Q88N37 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
FUM
5XNZ
A0A0K2JL82 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
MLI
2PFM
A0A6L8PR48 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
OXL
2X75
Q7A0G9 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
SIN
4EEI
Q5NIQ1 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=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.