Protein profile

KP13_00073

D-serine dehydratase

Genome: KpKP13

Gene: dsdA AHE41996.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYZ9
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Amino acids 443
Annotations 8
Features 22
PDB binders 0
Druggability 0.608

Overview

Basic information about this protein and its source genome.

Accession
KP13_00073
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
dsdA AHE41996.1
Status
annotated
Amino acids
443
Structure source
AlphaFold + ColabFold
EC
4.3.1.18
GO
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:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. GO:0046416 The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids. GO:0008721 Catalysis of the reaction: D-serine = pyruvate + NH4+. GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water. GO:0036088 The chemical reactions and pathways resulting in the breakdown of D-serine.

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
96.33

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 0.608
Structure A0A0H3GYZ9
Pocket Pocket 3
P2Rank 0.821
Structure A0A0H3GYZ9
Pocket Pocket 1
ColabFold model
FPocket 0.479 · Pocket 6
P2Rank 0.714 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 329 / 4744 genomes with a hit
Normalized 0.069

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • GO:0046416 The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids.
  • GO:0008721 Catalysis of the reaction: D-serine = pyruvate + NH4+.
  • GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
  • GO:0036088 The chemical reactions and pathways resulting in the breakdown of D-serine.
  • GO:0009097 OBSOLETE. The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
12 439 NCBIfam TIGR02035 D-serine ammonia-lyase
12 439 InterPro IPR011780 D-serine ammonia-lyase
26 432 CDD cd06447 D-Ser-dehyd
78 400 Pfam PF00291 Pyridoxal-phosphate dependent enzyme
78 400 InterPro IPR001926 Tryptophan synthase beta chain-like, PALP domain
1 443 Hamap MF_01030 D-serine dehydratase [dsdA].
1 443 InterPro IPR011780 D-serine ammonia-lyase
117 239 FunFam G3DSA:3.40.50.1100:FF:000018 D-serine dehydratase
92 440 PANTHER PTHR48078 THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED
117 239 Gene3D G3DSA:3.40.50.1100 -
117 239 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
18 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
109 123 ProSitePatterns PS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.
109 123 InterPro IPR000634 Serine/threonine dehydratase, pyridoxal-phosphate-binding site
23 443 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
7 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
99 438 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes
99 438 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
14 441 Gene3D G3DSA:3.40.50.1100 -
14 441 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily

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_A0A0H3GYZ9
AlphaFold — — full sequence — Viewing
ColabFold KP13_00073
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 0.608

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 12.56 0.655
2 2.71 0.081
3 2.18 0.052
4 1.66 0.028
5 1.11 0.008