Protein profile

KP13_31611

Propanediol utilization protein pduB

Genome: KpKP13

Gene: pduB AHE42889.1 Structure source: AlphaFold + ColabFold UniProt W9BN76
Export view
Amino acids 233
Annotations 2
Features 26
PDB binders 1
Druggability 0.215

Overview

Basic information about this protein and its source genome.

Accession
KP13_31611
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
pduB AHE42889.1
Status
annotated
Amino acids
233
Structure source
AlphaFold + ColabFold
GO
GO:0031469 An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy. GO:0005198 The action of a molecule that contributes to the structural integrity of a complex.

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
Unknown
ColabFold pLDDT
97.13

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 0.215
Structure W9BN76
Pocket Pocket 10
P2Rank 0.782
Structure W9BN76
Pocket Pocket 1
ColabFold model
FPocket 0.38 · Pocket 1
P2Rank 0.82 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 222 / 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.

2 GO

Gene Ontology (GO)

2
  • GO:0031469 An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy.
  • GO:0005198 The action of a molecule that contributes to the structural integrity of a complex.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
20 114 Gene3D G3DSA:3.30.70.1710 -
20 114 InterPro IPR037233 CcmK-like superfamily
1 233 PIRSF PIRSF012290 EutL_PduB
1 233 InterPro IPR009193 Bacterial microcompartment shell protein, EutL/PduB type
125 223 Gene3D G3DSA:3.30.70.1710 -
125 223 InterPro IPR037233 CcmK-like superfamily
10 115 ProSiteProfiles PS51931 Bacterial microcompartment (BMC) circularly permuted domain profile.
10 115 InterPro IPR044870 Bacterial microcompartment (BMC) circularly permuted domain
117 225 ProSiteProfiles PS51931 Bacterial microcompartment (BMC) circularly permuted domain profile.
117 225 InterPro IPR044870 Bacterial microcompartment (BMC) circularly permuted domain
149 218 CDD cd07048 BMC_PduB_repeat2
9 142 CDD cd07047 BMC_PduB_repeat1
148 217 SUPERFAMILY SSF143414 CcmK-like
148 217 InterPro IPR037233 CcmK-like superfamily
149 219 Pfam PF00936 BMC domain
149 219 InterPro IPR000249 Bacterial microcompartment domain
43 111 Pfam PF00936 BMC domain
43 111 InterPro IPR000249 Bacterial microcompartment domain
42 119 SUPERFAMILY SSF143414 CcmK-like
42 119 InterPro IPR037233 CcmK-like superfamily
42 124 SMART SM00877 BMC_2
42 124 InterPro IPR000249 Bacterial microcompartment domain
148 225 SMART SM00877 BMC_2
148 225 InterPro IPR000249 Bacterial microcompartment domain
9 233 NCBIfam TIGR04501 microcompartment protein PduB
9 233 InterPro IPR030984 Bacterial microcompartment shell protein PduB

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...

Legend High Medium Low

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_W9BN76
AlphaFold — — full sequence — Viewing
ColabFold KP13_31611
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
10 0.215
6 0.211

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 13.08 0.673
2 1.89 0.038

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

3 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
ETA
4TME
Q8XLZ0 61.1 Da LogP -1.06 TPSA 46.2 ✓ Ro5 ✓ Clean C(CO)N

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.