Protein profile

KP13_31803

glycine cleavage system aminomethyltransferase T

Genome: KpKP13

Gene: gcvT AHE42746.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H2N5
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Amino acids 375
Annotations 3
Features 22
PDB binders 5
Druggability 0.944

Overview

Basic information about this protein and its source genome.

Accession
KP13_31803
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
gcvT AHE42746.1
Status
annotated
Amino acids
375
Structure source
AlphaFold + ColabFold
GO
GO:0006546 The chemical reactions and pathways resulting in the breakdown of glycine. GO:0005515 Binding to a protein. GO:0004047 Catalysis of the reaction: N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4+.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
34.191
Human E-value
1.99e-39
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.98

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 0.944
Structure A0A0H3H2N5
Pocket Pocket 1
P2Rank 0.927
Structure A0A0H3H2N5
Pocket Pocket 1
ColabFold model
FPocket 0.979 · Pocket 12
P2Rank 0.932 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 144 / 4744 genomes with a hit
Normalized 0.03

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:0006546 The chemical reactions and pathways resulting in the breakdown of glycine.
  • GO:0005515 Binding to a protein.
  • GO:0004047 Catalysis of the reaction: N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4+.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
288 375 Gene3D G3DSA:2.40.30.110 -
18 265 Pfam PF01571 Aminomethyltransferase folate-binding domain
18 265 InterPro IPR006222 Aminomethyltransferase, folate-binding domain
282 372 SUPERFAMILY SSF101790 Aminomethyltransferase beta-barrel domain
282 372 InterPro IPR029043 Glycine cleavage T-protein/YgfZ, C-terminal
16 242 Gene3D G3DSA:3.30.1360.120 Probable tRNA modification gtpase trme; domain 1
16 242 InterPro IPR027266 GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1
243 287 Gene3D G3DSA:4.10.1250.10 Aminomethyltransferase fragment
4 374 PIRSF PIRSF006487 GCST
243 287 FunFam G3DSA:4.10.1250.10:FF:000001 Aminomethyltransferase
12 370 PANTHER PTHR43757 AMINOMETHYLTRANSFERASE
12 370 InterPro IPR028896 Aminomethyltransferase-like
62 150 FunFam G3DSA:3.30.70.1400:FF:000001 Aminomethyltransferase
288 375 FunFam G3DSA:2.40.30.110:FF:000001 Aminomethyltransferase
13 370 NCBIfam TIGR00528 glycine cleavage system aminomethyltransferase GcvT
13 370 InterPro IPR006223 Glycine cleavage system T protein
12 370 Hamap MF_00259 Aminomethyltransferase [gcvT].
12 370 InterPro IPR022903 Glycine cleavage system T protein, bacteria
14 288 SUPERFAMILY SSF103025 Folate-binding domain
291 367 Pfam PF08669 Glycine cleavage T-protein C-terminal barrel domain
291 367 InterPro IPR013977 Glycine cleavage T-protein, C-terminal barrel domain
62 149 Gene3D G3DSA:3.30.70.1400 -

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_A0A0H3H2N5
AlphaFold — — full sequence — Viewing
ColabFold KP13_31803
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 0.944

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 23.72 0.892

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
C2F
3A8I
P27248 459.5 Da LogP -0.26 TPSA 202.8 1 viol. ✓ Clean C[N@@]1[C@H](CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C…
FFO
1WOP
Q9WY54 473.4 Da LogP -0.73 TPSA 219.8 1 viol. ✓ Clean c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C…
FOA
2GAG
Q3ZDQ8 112.1 Da LogP 0.98 TPSA 50.4 ✓ Ro5 ✓ Clean c1cc(oc1)C(=O)O
RED
1WOR
Q9WY54 208.3 Da LogP 2.25 TPSA 37.3 ✓ Ro5 ✓ Clean C(CCC(=O)O)C[C@H](CCS)S
THG
4PAA
Q63342 445.4 Da LogP -0.28 TPSA 211.6 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…

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.