Protein profile

VK055_4065

cystathionine beta-lyase

Genome: KpATCC43816

Gene: AIK82612.1 metC3 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTB9
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Amino acids 382
Annotations 8
Features 18
PDB binders 6
Druggability 0.519

Overview

Basic information about this protein and its source genome.

Accession
VK055_4065
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82612.1 metC3
Status
annotated
Amino acids
382
Structure source
AlphaFold + ColabFold
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:0019346 The interconversion of homocysteine and cysteine via cystathionine. In contrast with enteric bacteria and mammals, Saccharomyces cerevisiae has two transsulfuration pathways employing two separate sets of enzymes. GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004123 Catalysis of the reaction: L-cystathionine + H2O = 2-oxobutanoate + L-cysteine + NH4+. GO:0003962 Catalysis of the reaction: L-cysteine + O-succinyl-L-homoserine = H+ + L,L-cystathionine + succinate.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
48.619
Human E-value
1.06e-109
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
42.328
DEG E-value
1.93e-103
Localization
Cytoplasmic
ColabFold pLDDT
97.05

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 0.519
Structure A0A0H3GTB9
Pocket Pocket 1
P2Rank 0.712
Structure A0A0H3GTB9
Pocket Pocket 1
ColabFold model
FPocket 0.647 · Pocket 1
P2Rank 0.684 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
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.

8 GO

Gene Ontology (GO)

8
  • 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:0019346 The interconversion of homocysteine and cysteine via cystathionine. In contrast with enteric bacteria and mammals, Saccharomyces cerevisiae has two transsulfuration pathways employing two separate sets of enzymes.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004123 Catalysis of the reaction: L-cystathionine + H2O = 2-oxobutanoate + L-cysteine + NH4+.
  • GO:0003962 Catalysis of the reaction: L-cysteine + O-succinyl-L-homoserine = H+ + L,L-cystathionine + succinate.
  • GO:0019343 OBSOLETE. The chemical reactions and pathways resulting in the formation of L-cysteine, via the intermediate L-cystathionine.
  • GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
1 382 PIRSF PIRSF001434 CGS
1 382 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
19 380 CDD cd00614 CGS_like
19 380 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
188 202 ProSitePatterns PS00868 Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.
188 202 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
4 380 PANTHER PTHR11808 TRANS-SULFURATION ENZYME FAMILY MEMBER
4 380 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
2 246 FunFam G3DSA:3.40.640.10:FF:000009 Cystathionine gamma-synthase homolog
13 380 SUPERFAMILY SSF53383 PLP-dependent transferases
13 380 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
247 381 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
247 381 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
248 381 FunFam G3DSA:3.90.1150.10:FF:000033 Cystathionine gamma-synthase
6 379 Pfam PF01053 Cys/Met metabolism PLP-dependent enzyme
6 379 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
2 246 Gene3D G3DSA:3.40.640.10 -
2 246 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain

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_A0A0H3GTB9
AlphaFold — — full sequence — Viewing
ColabFold VK055_4065
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 0.519
3 0.003
12 0.0
24 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 16.86 0.712
2 5.13 0.194

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.

32 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
0JO
4IYO
Q5H4T8 316.2 Da LogP 0.72 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/C(=C)C(=O)O)O
E9U
6LE4
F9UT53 451.4 Da LogP 0.11 TPSA 212.9 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H](CCSC[C@@H]…
F0G
6CJA
Q5ZX43 318.2 Da LogP 0.60 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H](C)C(=O)O)O
KOU
6LDO
F9UT53 334.2 Da LogP -0.43 TPSA 169.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/C(CO)C(=O)O)O
NAK
4IYO
Q5H4T8 87.1 Da LogP -3.04 TPSA 65.7 ✓ Ro5 ✓ Clean CC(=[NH2+])C(=O)[O-]
PYR
6K1L
B4SII9 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=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.