Protein profile

KP13_05370

PKHD-type hydroxylase

Genome: KpKP13

Gene: AHE45016.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRM2
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Amino acids 224
Annotations 4
Features 14
PDB binders 0
Druggability 0.621

Overview

Basic information about this protein and its source genome.

Accession
KP13_05370
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45016.1
Status
annotated
Amino acids
224
Structure source
AlphaFold + ColabFold
GO
GO:0005506 Binding to an iron (Fe) ion. GO:0016705 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor. GO:0031418 Binding to L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species. GO:0016706 Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.

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
95.25

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 0.621
Structure A0A0H3GRM2
Pocket Pocket 1
P2Rank 0.887
Structure A0A0H3GRM2
Pocket Pocket 1
ColabFold model
FPocket 0.721 · Pocket 1
P2Rank 0.897 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 57 / 4744 genomes with a hit
Normalized 0.012

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0016705 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
  • GO:0031418 Binding to L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
  • GO:0016706 Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
1 175 SMART SM00702 p4hc
1 175 InterPro IPR006620 Prolyl 4-hydroxylase, alpha subunit
181 223 Pfam PF18331 PKHD-type hydroxylase C-terminal domain
181 223 InterPro IPR041097 PKHD-type hydroxylase C-terminal domain
77 176 ProSiteProfiles PS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.
77 176 InterPro IPR005123 Oxoglutarate/iron-dependent dioxygenase
1 224 PANTHER PTHR41536 PKHD-TYPE HYDROXYLASE YBIX
1 224 InterPro IPR023550 PKHD-type hydroxylase
178 224 Gene3D G3DSA:4.10.860.20 Rabenosyn, Rab binding domain
1 176 FunFam G3DSA:2.60.120.620:FF:000006 PKHD-type hydroxylase YbiX
83 174 Pfam PF13640 2OG-Fe(II) oxygenase superfamily
83 174 InterPro IPR044862 Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain
1 224 Hamap MF_00657 PKHD-type hydroxylase YbiX [ybiX].
1 176 Gene3D G3DSA:2.60.120.620 q2cbj1_9rhob like domain

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_A0A0H3GRM2
AlphaFold — — full sequence — Viewing
ColabFold KP13_05370
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 0.621
11 0.27
14 0.067
3 0.003

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 28.08 0.887