Protein profile

VK055_0187

PLD-like domain protein

Genome: KpATCC43816

Gene: AIK78815.1 Structure source: AlphaFold + ColabFold UniProt A0A483NZE1
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Amino acids 625
Annotations 3
Features 12
PDB binders 0
Druggability 0.491

Overview

Basic information about this protein and its source genome.

Accession
VK055_0187
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK78815.1
Status
annotated
Amino acids
625
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:0004630 A glycerophospholipase activity that cleaves the second phosphodiester bond between the phosphate and phospholipid, releasing a phosphatidic acid. GO:0009395 The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.

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
91.05

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 0.491
Structure A0A483NZE1
Pocket Pocket 43
P2Rank 0.931
Structure A0A483NZE1
Pocket Pocket 1
ColabFold model
FPocket 0.103 · Pocket 30
P2Rank 0.91 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 1 / 4744 genomes with a hit
Normalized 0

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: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:0004630 A glycerophospholipase activity that cleaves the second phosphodiester bond between the phosphate and phospholipid, releasing a phosphatidic acid.
  • GO:0009395 The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
515 606 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A
518 545 ProSiteProfiles PS50035 Phospholipase D phosphodiesterase active site profile.
518 545 InterPro IPR001736 Phospholipase D/Transphosphatidylase
40 588 PANTHER PTHR18896 PHOSPHOLIPASE D
40 588 InterPro IPR015679 Phospholipase D family
518 545 SMART SM00155 pld_4
215 247 SMART SM00155 pld_4
215 247 InterPro IPR001736 Phospholipase D/Transphosphatidylase
23 311 SUPERFAMILY SSF56024 Phospholipase D/nuclease
467 487 Coils Coil Coil
339 572 SUPERFAMILY SSF56024 Phospholipase D/nuclease
24 328 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A

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

Loading 3D structure...

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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_A0A483NZE1
AlphaFold — — full sequence — Viewing
ColabFold VK055_0187
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
43 0.491
27 0.029
1 0.004
16 0.001

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 35.22 0.931
2 7.07 0.307
3 4.01 0.13
4 2.38 0.051
5 2.16 0.042