Protein profile

VK055_4093

alanine racemase, N-terminal domain protein

Genome: KpATCC43816

Gene: AIK82639.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVD8
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Amino acids 233
Annotations 1
Features 18
PDB binders 0
Druggability 0.873

Overview

Basic information about this protein and its source genome.

Accession
VK055_4093
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82639.1
Status
annotated
Amino acids
233
Structure source
AlphaFold + ColabFold
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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
66.667
Human E-value
9.32e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
62.5
DEG E-value
2.48e-97
Localization
Cytoplasmic
ColabFold pLDDT
96.0

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 0.873
Structure A0A0H3GVD8
Pocket Pocket 1
P2Rank 0.208
Structure A0A0H3GVD8
Pocket Pocket 1
ColabFold model
FPocket 0.554 · Pocket 3
P2Rank 0.156 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 223 / 4744 genomes with a hit
Normalized 0.047

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
6 228 Hamap MF_02087 Pyridoxal phosphate homeostasis protein.
6 228 InterPro IPR011078 Pyridoxal phosphate homeostasis protein
79 93 ProSitePatterns PS01211 Uncharacterized protein family UPF0001 signature.
79 93 InterPro IPR011078 Pyridoxal phosphate homeostasis protein
1 228 FunFam G3DSA:3.20.20.10:FF:000004 Pyridoxal phosphate homeostasis protein
5 229 Pfam PF01168 Alanine racemase, N-terminal domain
5 229 InterPro IPR001608 Alanine racemase, N-terminal
1 229 NCBIfam TIGR00044 YggS family pyridoxal phosphate-dependent enzyme
1 229 InterPro IPR011078 Pyridoxal phosphate homeostasis protein
1 227 SUPERFAMILY SSF51419 PLP-binding barrel
1 227 InterPro IPR029066 PLP-binding barrel
1 228 Gene3D G3DSA:3.20.20.10 Alanine racemase
1 228 InterPro IPR029066 PLP-binding barrel
1 233 PIRSF PIRSF004848 YBL036c_PLPDEIII
1 233 InterPro IPR011078 Pyridoxal phosphate homeostasis protein
3 233 PANTHER PTHR10146 PROLINE SYNTHETASE CO-TRANSCRIBED BACTERIAL HOMOLOG PROTEIN
3 233 InterPro IPR011078 Pyridoxal phosphate homeostasis protein
3 228 CDD cd06824 PLPDE_III_Yggs_like

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_A0A0H3GVD8
AlphaFold — — full sequence — Viewing
ColabFold VK055_4093
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 0.873
10 0.556

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 2.47 0.068
2 1.08 0.007