Protein profile

VK055_3869

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase

Genome: KpATCC43816

Gene: yrbI AIK82419.1 Structure source: Experimental + ColabFold UniProt A0A0H3GTS8
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Amino acids 188
Annotations 6
Features 17
PDB binders 0
Druggability 0.287

Overview

Basic information about this protein and its source genome.

Accession
VK055_3869
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
yrbI AIK82419.1
Status
annotated
Amino acids
188
Structure source
Experimental + ColabFold
EC
3.1.3.45
GO
GO:0016788 Catalysis of the hydrolysis of any ester bond. GO:0019143 Catalysis of the reaction: 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + H2O = 3-deoxy-D-manno-octulosonate + phosphate. GO:0046872 Binding to a metal ion. GO:0008781 Catalysis of the reaction: CTP + N-acylneuraminate = diphosphate + CMP-N-acylneuraminate. GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.335
Human E-value
1.02e-18
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
57.062
DEG E-value
3.2000000000000004e-64
Localization
Cytoplasmic
ColabFold pLDDT
96.57

Selected Druggability evidence

PDB experimental structure

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 0.287
Structure 7T35
Pocket Pocket 5
P2Rank 0.021
Structure 7T35
Pocket Pocket 1
ColabFold model
FPocket 0.557 · Pocket 2
P2Rank 0.127 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 144 / 4744 genomes with a hit
Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0016788 Catalysis of the hydrolysis of any ester bond.
  • GO:0019143 Catalysis of the reaction: 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + H2O = 3-deoxy-D-manno-octulosonate + phosphate.
  • GO:0046872 Binding to a metal ion.
  • GO:0008781 Catalysis of the reaction: CTP + N-acylneuraminate = diphosphate + CMP-N-acylneuraminate.
  • GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
13 188 PIRSF PIRSF006118 KDO8-P_Ptase
13 188 InterPro IPR010023 KdsC family
7 188 FunFam G3DSA:3.40.50.1000:FF:000029 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
21 181 SFLD SFLDG01138 C1.6.2: Deoxy-d-mannose-octulosonate 8-phosphate Phosphatase Like
21 181 InterPro IPR010023 KdsC family
26 171 CDD cd01630 HAD_KDO-like
27 142 NCBIfam TIGR01662 HAD-IIIA family hydrolase
27 142 InterPro IPR006549 HAD-superfamily hydrolase,subfamily IIIA
94 162 Pfam PF08282 haloacid dehalogenase-like hydrolase
24 180 PANTHER PTHR21485 HAD SUPERFAMILY MEMBERS CMAS AND KDSC
1 188 Gene3D G3DSA:3.40.50.1000 -
1 188 InterPro IPR023214 HAD superfamily
26 178 NCBIfam TIGR01670 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family
26 178 InterPro IPR010023 KdsC family
22 181 SUPERFAMILY SSF56784 HAD-like
22 181 InterPro IPR036412 HAD-like superfamily
21 181 SFLD SFLDS00003 Haloacid Dehalogenase

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

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 7T35
X-ray 2.65 Å A
100.0% 1-188
PDBe RCSB PDBj File
Viewing
ColabFold VK055_3869
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
5 0.287
1 0.265

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 1.5 0.021
2 1.23 0.011