Protein profile

VK055_3384

D-serine ammonia-lyase

Genome: KpATCC43816

Gene: AIK81941.1 dsdA Structure source: AlphaFold + ColabFold UniProt A0A0H3GYZ9
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Amino acids 442
Annotations 8
Features 17
PDB binders 0
Druggability 0.608

Overview

Basic information about this protein and its source genome.

Accession
VK055_3384
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK81941.1 dsdA
Status
annotated
Amino acids
442
Structure source
AlphaFold + ColabFold
EC
4.3.1.18
GO
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:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. 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: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
96.2

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 0.336 · Pocket 1
P2Rank 0.679 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 330 / 4744 genomes with a hit
Normalized 0.07

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: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:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • 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: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.

17 records
Show feature table
Start End DB Term Name
77 439 PANTHER PTHR48078 THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED
25 431 CDD cd06447 D-Ser-dehyd
108 122 ProSitePatterns PS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.
108 122 InterPro IPR000634 Serine/threonine dehydratase, pyridoxal-phosphate-binding site
13 440 Gene3D G3DSA:3.40.50.1100 -
13 440 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
1 442 Hamap MF_01030 D-serine dehydratase [dsdA].
1 442 InterPro IPR011780 D-serine ammonia-lyase
98 437 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes
98 437 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
116 238 Gene3D G3DSA:3.40.50.1100 -
116 238 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
74 399 Pfam PF00291 Pyridoxal-phosphate dependent enzyme
74 399 InterPro IPR001926 Tryptophan synthase beta chain-like, PALP domain
116 238 FunFam G3DSA:3.40.50.1100:FF:000018 D-serine dehydratase
11 438 NCBIfam TIGR02035 D-serine ammonia-lyase
11 438 InterPro IPR011780 D-serine ammonia-lyase

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 VK055_3384
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
5 0.003
10 0.002
9 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 22.05 0.821
2 4.64 0.166
3 3.76 0.117
4 2.65 0.063
5 2.05 0.038