Protein profile

KP13_01871

S-adenosylmethionine decarboxylase proenzyme

Genome: KpKP13

Gene: speD AHE46311.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GIB3
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Amino acids 264
Annotations 4
Features 14
PDB binders 0
Druggability 0.515

Overview

Basic information about this protein and its source genome.

Accession
KP13_01871
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
speD AHE46311.1
Status
annotated
Amino acids
264
Structure source
AlphaFold + ColabFold
EC
4.1.1.50
GO
GO:0008295 The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane. GO:0004014 Catalysis of the reaction: S-adenosyl-L-methionine + H+ = S-adenosylmethioninamine + CO2. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
87.49

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 0.515
Structure A0A0H3GIB3
Pocket Pocket 3
P2Rank 0.306
Structure A0A0H3GIB3
Pocket Pocket 1
ColabFold model
FPocket 0.919 · Pocket 2
P2Rank 0.319 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 443 / 4744 genomes with a hit
Normalized 0.093

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0008295 The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
  • GO:0004014 Catalysis of the reaction: S-adenosyl-L-methionine + H+ = S-adenosylmethioninamine + CO2.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
1 263 PIRSF PIRSF001356 SAM_decarboxylas
1 263 InterPro IPR009165 S-adenosylmethionine decarboxylase, bacterial
32 185 FunFam G3DSA:3.60.90.10:FF:000001 S-adenosylmethionine decarboxylase proenzyme
41 173 SUPERFAMILY SSF56276 S-adenosylmethionine decarboxylase
41 173 InterPro IPR016067 S-adenosylmethionine decarboxylase, core
33 169 Pfam PF02675 S-adenosylmethionine decarboxylase
33 169 InterPro IPR003826 S-adenosylmethionine decarboxylase family, prokaryotic
3 261 NCBIfam TIGR03331 adenosylmethionine decarboxylase
3 261 InterPro IPR009165 S-adenosylmethionine decarboxylase, bacterial
1 194 PANTHER PTHR33866 S-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME
1 194 InterPro IPR003826 S-adenosylmethionine decarboxylase family, prokaryotic
32 185 Gene3D G3DSA:3.60.90.10 -
1 264 Hamap MF_00465 S-adenosylmethionine decarboxylase proenzyme [speD].
1 264 InterPro IPR009165 S-adenosylmethionine decarboxylase, bacterial

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_A0A0H3GIB3
AlphaFold — — full sequence — Viewing
ColabFold KP13_01871
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
3 0.515

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 6.3 0.316
2 1.21 0.011