Protein profile

VK055_2392

periplasmic vitamin B12 binding protein

Genome: KpATCC43816

Gene: AIK80989.1 yadT Structure source: AlphaFold + ColabFold UniProt A0A0H3GII9
Export view
Amino acids 266
Annotations 3
Features 21
PDB binders 0
Druggability 0.384

Overview

Basic information about this protein and its source genome.

Accession
VK055_2392
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80989.1 yadT
Status
annotated
Amino acids
266
Structure source
AlphaFold + ColabFold
GO
GO:0031419 Binding to cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. GO:0015889 The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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
92.51

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 0.384
Structure A0A0H3GII9
Pocket Pocket 11
P2Rank 0.281
Structure A0A0H3GII9
Pocket Pocket 1
ColabFold model
FPocket 0.499 · Pocket 6
P2Rank 0.588 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 106 / 4744 genomes with a hit
Normalized 0.022

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:0031419 Binding to cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
  • GO:0015889 The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
23 266 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 39 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
2 266 Hamap MF_01000 Vitamin B12-binding protein [btuF].
2 266 InterPro IPR023544 ABC transporter, vitamin B12-binding protein
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
17 264 PANTHER PTHR42860 VITAMIN B12-BINDING PROTEIN
25 266 ProSiteProfiles PS50983 Iron siderophore/cobalamin periplasmic-binding domain profile.
25 266 InterPro IPR002491 ABC transporter periplasmic binding domain
21 139 Gene3D G3DSA:3.40.50.1980 Nitrogenase molybdenum iron protein domain
26 225 Pfam PF01497 Periplasmic binding protein
26 225 InterPro IPR002491 ABC transporter periplasmic binding domain
25 217 NCBIfam NF038402 helical backbone metal receptor
141 266 Gene3D G3DSA:3.40.50.1980 Nitrogenase molybdenum iron protein domain
1 22 SignalP_EUK SignalP-noTM SignalP-noTM
25 262 SUPERFAMILY SSF53807 Helical backbone metal receptor
1 22 SignalP_GRAM_NEGATIVE SignalP-TM SignalP-TM
16 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
25 260 CDD cd01144 BtuF

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_A0A0H3GII9
AlphaFold — — full sequence — Viewing
ColabFold VK055_2392
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
3 0.069
1 0.022
15 0.002
4 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 6.59 0.281
2 3.55 0.105