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Zinc finger protein 492

Reviewed
Reference proteome

AF-Q9P255-F1-v4

DownloadPDB file mmCIF file Predicted aligned error

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Information

Structure viewer
 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.

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SequenceNo structure available
Structure Tools
  • 2:07:40
    Mol* Plugin 4.5.0 [8/22/2024, 2:35:37 PM]
 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.

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Scored residueAligned residue
01002003004005000100200300400500
  • 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.

The heatmap is unavailable for mobile devices. Please use a larger screen to see the heatmap.

153150100150200250300350400450500200400
50100150200250300350400450500GAVLISTCMDNEQRKHFYWPGAVLISTCMDNEQRKHFYWPAlternative amino acidsResidue sequence number
BenignUncertainPathogenic Reference
Amino acid present in the reference UniProt protein sequence, based on HG38
  • 0.0
  • 0.2
  • 0.3
  • 0.4
  • 0.5
  • 0.6
  • 0.7
  • 0.8
  • 1.0
  • -
Filter by category
0
0.34
0.00.34
0.34
0.56
0.340.564
0.56
1
0.5641
Similar structures Discover similar structures from the Protein Data Bank (PDB) and the AlphaFold Database clustered to 50% sequence identity (AFDB50) using Foldseek.
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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-A0A821QZ91-F1
Unreviewed
Reference proteome
Description (mimic poison frog) hypothetical protein

(mimic poison frog) hypothetical protein ...

(mimic poison frog) hypothetical protein
SpeciesRanitomeya imitator (mimic poison frog)

Ranitomeya imitator (mimic poison frog)...

Ranitomeya imitator (mimic poison frog)
Sequence length 549 Average pLDDT 81
AFDB accessionAF-A0A2D0S883-F1
Unreviewed
Reference proteome
Description zinc finger protein 501-like isoform X3

zinc finger protein 501-like isoform X3 ...

zinc finger protein 501-like isoform X3
SpeciesIctalurus punctatus
Ictalurus punctatus
Sequence length 513 Average pLDDT 79.75
AFDB accessionAF-A0A2D0S940-F1
Unreviewed
Reference proteome
Description zinc finger protein 501-like isoform X4

zinc finger protein 501-like isoform X4 ...

zinc finger protein 501-like isoform X4
SpeciesIctalurus punctatus
Ictalurus punctatus
Sequence length 510 Average pLDDT 78.81
AFDB accessionAF-E9Q459-F1
Unreviewed
Reference proteome
Description Zinc finger protein 160
Zinc finger protein 160
SpeciesMus musculus
Mus musculus
Sequence length 650 Average pLDDT 76.15
AFDB accessionAF-F7DCN0-F1
Unreviewed
Reference proteome
Description Uncharacterized protein
Uncharacterized protein
SpeciesMonodelphis domestica
Monodelphis domestica
Sequence length 540 Average pLDDT 76.12
AFDB accessionAF-A0A2D0S892-F1
Unreviewed
Reference proteome
Description zinc finger protein 709-like isoform X1

zinc finger protein 709-like isoform X1 ...

zinc finger protein 709-like isoform X1
SpeciesIctalurus punctatus
Ictalurus punctatus
Sequence length 542 Average pLDDT 75.5
AFDB accessionAF-A0A2D0S881-F1
Unreviewed
Reference proteome
Description zinc finger protein 420-like isoform X2

zinc finger protein 420-like isoform X2 ...

zinc finger protein 420-like isoform X2
SpeciesIctalurus punctatus
Ictalurus punctatus
Sequence length 514 Average pLDDT 75.12
AFDB accessionAF-A0A6P5NZJ3-F1
Unreviewed
Reference proteome
Description zinc finger protein 431-like
zinc finger protein 431-like
SpeciesMus caroli
Mus caroli
Sequence length 620 Average pLDDT 74.06
AFDB accessionAF-Q9P255-F1
Reviewed (Swiss-Prot)
Reference proteome
Description Zinc finger protein 492
Zinc finger protein 492
SpeciesHomo sapiens
Homo sapiens
Sequence length 531 Average pLDDT 73.86
AFDB accessionAF-Q8N8J6-F1
Reviewed (Swiss-Prot)
Reference proteome
Description Zinc finger protein 615
Zinc finger protein 615
SpeciesHomo sapiens
Homo sapiens
Sequence length 731 Average pLDDT 73.5
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Help

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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.

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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.

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