New!
Explore similar structures
New!
Find similar folds in PDB and AFDB with Foldseek

Autoinducer 2-binding periplasmic protein LuxP

Unreviewed
Reference proteome

AF-A0A6B8NJ26-F1-v4

DownloadPDB file mmCIF file Predicted aligned error

Share your feedback on structure with Google DeepMind Looks great Could be improved

Information

Structure viewer
Model Confidence
pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test (lDDT-Cα). It is a measure of local accuracy - for interpreting larger scale features like relative domain positions see the “predicted aligned error” plot and corresponding tutorial. Confidence bands are used to colour-code the residues in the 3D viewer. The exact pLDDT value is shown when you mouseover the structure or the sequence. It can also be found in the B-factor fields of the downloadable coordinate files.

 Very high (pLDDT > 90)
 High (90 > pLDDT > 70)
 Low (70 > pLDDT > 50)
 Very low (pLDDT < 50)
AlphaFold produces a per-residue model confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.

WebGL does not seem to be available.

This can be caused by an outdated browser, graphics card driver issue, or bad weather. Sometimes, just restarting the browser helps. Also, make sure hardware acceleration is enabled in your browser.

For a list of supported browsers, refer to http://caniuse.com/#feat=webgl.

SequenceNo structure available
Structure Tools
  • 8:21:38
    Mol* Plugin 4.5.0 [8/22/2024, 2:35:37 PM]
Model Confidence
pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test (lDDT-Cα). It is a measure of local accuracy - for interpreting larger scale features like relative domain positions see the “predicted aligned error” plot and corresponding tutorial. Confidence bands are used to colour-code the residues in the 3D viewer. The exact pLDDT value is shown when you mouseover the structure or the sequence. It can also be found in the B-factor fields of the downloadable coordinate files.
 Very high (pLDDT > 90)
 High (90 > pLDDT > 70)
 Low (70 > pLDDT > 50)
 Very low (pLDDT < 50)
AlphaFold produces a per-residue model confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.
Scored residueAligned residue
050100150200250050100150200250
  • 0
  • 5
  • 10
  • 15
  • 20
  • 25
  • 30
Expected position error (Ångströms)

Predicted aligned error (PAE)

Click and drag a box on the PAE viewer to select regions of the structure and highlight them on the 3D viewer.

PAE data is useful for assessing inter-domain accuracy – go to Help section below for more information.

Similar structures Discover similar structures from the Protein Data Bank (PDB) and the AlphaFold Database clustered to 50% sequence identity (AFDB50) using Foldseek.
Explore similar structures
Structure search is powered by Foldseek, a tool for fast protein structure comparison. 
Start a structural similarity search to discover similar proteins.
Structure similarity clusterPredicted structures in the AlphaFold Protein Structure Database clustered using MMseqs2 and Foldseek. This data is provided by the AFDB Clusters.

AlphaFold database protein sequences clustered by the MMseqs2 algorithm (Steinegger M. and Soeding J., Nat. Commun. 9, 2018). Each cluster is comprised of sequences that fulfil two criteria: maintaining a maximum sequence identity of 50% and achieving a 90% bi-directional sequence overlap with the longest sequence of the cluster representative.

AFDB accession DescriptionSpecies
Sequence length
Average pLDDT
AFDB accessionAF-A0A659YPD2-F1
Unreviewed
Reference proteome
Description D-ribose ABC transporter substrate-binding protein

D-ribose ABC transporter substrate-binding protein ...

D-ribose ABC transporter substrate-binding protein
SpeciesMesorhizobium sp
Mesorhizobium sp
Sequence length 185 Average pLDDT 98.25
AFDB accessionAF-D0Z4Q3-F1
Unreviewed
Reference proteome
Description Autoinducer 2-binding periplasmic protein LuxP

Autoinducer 2-binding periplasmic protein LuxP ...

Autoinducer 2-binding periplasmic protein LuxP
SpeciesPhotobacterium damselae subsp. damselae CIP 102761

Photobacterium damselae subsp. damselae CIP 102761...

Photobacterium damselae subsp. damselae CIP 102761
Sequence length 266 Average pLDDT 98.06
AFDB accessionAF-A0A3S1Z5X0-F1
Unreviewed
Reference proteome
Description D-ribose ABC transporter substrate-binding protein

D-ribose ABC transporter substrate-binding protein ...

D-ribose ABC transporter substrate-binding protein
SpeciesMesorhizobium sp. M7D.F.Ca.US.004.03.1.1

Mesorhizobium sp. M7D.F.Ca.US.004.03.1.1...

Mesorhizobium sp. M7D.F.Ca.US.004.03.1.1
Sequence length 208 Average pLDDT 98.06
AFDB accessionAF-A0A531MMB6-F1
Unreviewed
Reference proteome
Description D-ribose ABC transporter substrate-binding protein

D-ribose ABC transporter substrate-binding protein ...

D-ribose ABC transporter substrate-binding protein
SpeciesMesorhizobium sp
Mesorhizobium sp
Sequence length 210 Average pLDDT 98.06
AFDB accessionAF-A0A3M8F4J0-F1
Unreviewed
Reference proteome
Description D-ribose ABC transporter substrate-binding protein

D-ribose ABC transporter substrate-binding protein ...

D-ribose ABC transporter substrate-binding protein
SpeciesStreptomyces xinghaiensis
Streptomyces xinghaiensis
Sequence length 284 Average pLDDT 97.81
AFDB accessionAF-A0A447LNR0-F1
Unreviewed
Reference proteome
Description Sugar ABC transporter substrate-binding protein

Sugar ABC transporter substrate-binding protein ...

Sugar ABC transporter substrate-binding protein
SpeciesAtlantibacter hermannii
Atlantibacter hermannii
Sequence length 246 Average pLDDT 97.75
AFDB accessionAF-A0A2N5AHK3-F1
Unreviewed
Reference proteome
Description D-ribose ABC transporter substrate-binding protein

D-ribose ABC transporter substrate-binding protein ...

D-ribose ABC transporter substrate-binding protein
SpeciesKlebsiella variicola
Klebsiella variicola
Sequence length 273 Average pLDDT 97.69
AFDB accessionAF-A0A378CD12-F1
Unreviewed
Reference proteome
Description Ribose ABC transport system
Ribose ABC transport system
SpeciesKlebsiella pneumoniae
Klebsiella pneumoniae
Sequence length 252 Average pLDDT 97.56
AFDB accessionAF-A0A378DIN8-F1
Unreviewed
Reference proteome
Description Ribose ABC transport system
Ribose ABC transport system
SpeciesKlebsiella pneumoniae subsp. rhinoscleromatis

Klebsiella pneumoniae subsp. rhinoscleromatis...

Klebsiella pneumoniae subsp. rhinoscleromatis
Sequence length 252 Average pLDDT 97.5
AFDB accessionAF-A0A2N2BJ80-F1
Unreviewed
Reference proteome
Description Ribose ABC transporter substrate-binding protein RbsB

Ribose ABC transporter substrate-binding protein RbsB ...

Ribose ABC transporter substrate-binding protein RbsB
SpeciesFirmicutes bacterium HGW-Firmicutes-3

Firmicutes bacterium HGW-Firmicutes-3...

Firmicutes bacterium HGW-Firmicutes-3
Sequence length 272 Average pLDDT 97.5
Items per page:
1 – 10 of 25278

Help

Visit our online training course

How to interpret the Predicted Aligned Error

 

The Predicted Aligned Error (PAE) measures the confidence in the relative position of two residues within the predicted structure, providing insight into the reliability of relative position and orientations of different domains. Consider the human protein encoded by the gene GNE (Q9Y223).

GNE has two distinct domains according to experimentally determined structures in the Protein Data Bank (PDBe-KB). Does AlphaFold confidently predict their relative positions? We can use the interactive Predicted Aligned Error (PAE) plot to answer this question.

The PAE plot is not an inter-residue distance map or a contact map. Instead, the shade of green indicates the expected distance error in Ångströms (Å), ranging from 0 Å to an arbitrary cut-off of 31 Å. The colour at (x, y) corresponds to the expected distance error in the residue x’s position when the predicted and the true structures are aligned on residue y.

A dark green tile corresponds to a good prediction (low error), whereas a light green tile indicates poor prediction (high error). For example, when aligning on residue 300:

  • We’re confident in the relative position of residue 200
  • We’re not confident in the relative position of residue 600

The two low-error, dark green squares correspond to the two domains. By clicking and dragging, you can highlight these squares on the structure. If you want to remove the highlighting, click the cross icon.

When selecting an off-diagonal region, the plot visually represents the relationship between the selected ranges on the sequence and structure. The x range corresponds to the selection for scored residues, highlighted in orange, while the y range of aligned residues is highlighted in emerald green.

The high PAE values across the whole inter-domain region indicate that for this particular protein, AlphaFold does not reliably predict the relative position of the domains.

Let’s consider another inter-domain example, the human protein encoded by DIP2B (Q9P265).

In this case, we have confidence in the relative position of scored residues around 1450 when aligned with residues around 850, suggesting a packing between the small central domains.

Note that the PAE scores are asymmetrical, meaning there might be variations in PAE values between (x,y) and (y,x) positions. This is particularly relevant for loop regions with highly uncertain orientations, as seen on the DNA topoisomerase 3 (Q8T2T7).

 


Last updated

Last updated in AlphaFold DB version 2022-11-01, created with the AlphaFold Monomer v2.0 pipeline.

Licence and attribution

Data is available for academic and commercial use, under a CC-BY-4.0 licence.

EMBL-EBI expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice.

If you make use of an AlphaFold prediction, please cite the following papers:
Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021).
Varadi, M et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Research (2024).
If you use data from AlphaMissense in your work, please cite the following paper:
Cheng, J et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science (2023).

AlphaFold Data Copyright (2022) DeepMind Technologies Limited.
AlphaMissense Copyright (2023) DeepMind Technologies Limited.

Feedback and questions

If you want to share feedback on an AlphaFold structure prediction, consider using the feedback buttons at the top of each structure page. If you have any questions that are not covered in the FAQs, please contact alphafold@deepmind.com. If you have feedback on the website or experience any bugs please contact afdbhelp@ebi.ac.uk.

Let us know how the AlphaFold Protein Structure Database has been useful in your research at alphafold@deepmind.com.

Disclaimer

The AlphaFold and AlphaMissense Data and other information provided on this site contain predictions with varying levels of confidence, is for theoretical modelling only and caution should be exercised in its use. It is provided 'as-is' without any warranty of any kind, whether expressed or implied. For clarity, no warranty is given that use of the information shall not infringe the rights of any third party. The information is not intended to be a substitute for professional medical advice, diagnosis, or treatment, and does not constitute medical or other professional advice. The AlphaFold and AlphaMissense Data have not been validated for, and are not approved for, any clinical use.

Use of the AlphaFold Protein Structure Database is subject to EMBL-EBI Terms of Use.