Syndecan-4

reviewed Reviewed
ref Reference proteome

AF-P49416-F1-v4

DownloadPDB file mmCIF file Predicted aligned error

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Mol* 3D 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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  • 18:46:13
    Mol* Plugin 4.17.0 [5/28/2025, 11:00:04 AM]
 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.

TED Domains and Predicted Aligned Error (PAE)

Scored residueAligned residue
050100150050100150
paescale
  • 0
  • 5
  • 10
  • 15
  • 20
  • 25
  • 30
Expected position error (Ångströms)
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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.

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AFDB accession DescriptionSpecies
Sequence length
Average pLDDT
AFDB accessionAF-A0A6J3DXL9-F1
unreviewed Unreviewed
ref Reference proteome
Description Syndecan
Syndecan
SpeciesAythya fuligula
Aythya fuligula
Sequence length 198 Average pLDDT 60.44
AFDB accessionAF-A0A091SBP0-F1
unreviewed Unreviewed
Description Syndecan
Syndecan
SpeciesNestor notabilis
Nestor notabilis
Sequence length 175 Average pLDDT 60.22
AFDB accessionAF-Q5I5K4-F1
unreviewed Unreviewed
Description Syndecan
Syndecan
SpeciesMeleagris gallopavo
Meleagris gallopavo
Sequence length 197 Average pLDDT 60.22
AFDB accessionAF-A0A091HS53-F1
unreviewed Unreviewed
Description Syndecan
Syndecan
SpeciesCalypte anna
Calypte anna
Sequence length 176 Average pLDDT 60.19
AFDB accessionAF-A0A7L2FXA0-F1
unreviewed Unreviewed
ref Reference proteome
Description Syndecan
Syndecan
SpeciesNyctibius grandis
Nyctibius grandis
Sequence length 176 Average pLDDT 60.09
AFDB accessionAF-A0A851PZW3-F1
unreviewed Unreviewed
ref Reference proteome
Description SDC4 protein
SDC4 protein
SpeciesAnhinga anhinga
Anhinga anhinga
Sequence length 176 Average pLDDT 60.03
AFDB accessionAF-A0A7L0TES4-F1
unreviewed Unreviewed
ref Reference proteome
Description Syndecan
Syndecan
SpeciesPodilymbus podiceps
Podilymbus podiceps
Sequence length 176 Average pLDDT 60
AFDB accessionAF-A0A7L0E9J7-F1
unreviewed Unreviewed
ref Reference proteome
Description Syndecan
Syndecan
SpeciesTrogon melanurus
Trogon melanurus
Sequence length 173 Average pLDDT 60
AFDB accessionAF-A0A093J4R3-F1
unreviewed Unreviewed
Description Syndecan
Syndecan
SpeciesFulmarus glacialis
Fulmarus glacialis
Sequence length 176 Average pLDDT 59.94
AFDB accessionAF-A0A851WFL1-F1
unreviewed Unreviewed
ref Reference proteome
Description SDC4 protein
SDC4 protein
SpeciesCorvus moneduloides (New Caledonian crow)

Corvus moneduloides (New Caledonian crow)...

Corvus moneduloides (New Caledonian crow)
Sequence length 176 Average pLDDT 59.94
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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).

pae image 1pae image 2

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.

pae image 3

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
pae image 4

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.

pae image 5pae image 6

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.

pae image 7pae image 8

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

pae image 8pae image 8

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.

pae image 8pae image 8

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).

pae image 8pae image 8
 


How to use The Encyclopedia of Domains

 

The Encyclopedia of Domains (TED) is a comprehensive resource that identifies and classifies protein domains within the AlphaFold Database using deep learning-based domain parsing and structure comparison. TED domains that share significant structural similarity with a previously characterised CATH domain are labelled with their predicted classification at the Topology/Fold level (3-level C.A.T. identifier) or Homologous Superfamily level (4-level C.A.T.H. identifier). Domains without classification labels indicate no similarity to CATH domains used during TED’s classification workflow.

You can visualise TED Domains in the AlphaFold database entries in both the Mol* 3D Viewer and the domain annotation track displayed above the interactive PAE plot. Hovering and clicking on an individual domain track opens a tooltip with details such as the total number of residues (length), its position within the protein sequence (boundaries), the average pLDDT score, the 3-level C.A.T or 4-level C.A.T.H classification identifier and a quality metric for the domain assignment. Learn more in our FAQ.

Let’s explore some examples:

Hemoglobin subunit gamma-1 (AF-P69891-F1). This protein’s PAE shows high confidence in the relative positions of almost all residues. TED identifies one domain, spanning residues 5 to 142, with a superfamily assignment.

ted image 1

Note that the Domain annotation track and the Mol* 3D Viewer structure colourings are mapped to individual domain boundaries and not classification levels. Therefore, an entry with multiple domains of the same Fold or Homologous Superfamily will show different colours for each domain. For example, the Bacterial Ig-like domain family protein (AF-A0A009R2D9-F1) contains twelve domains of varying quality, mostly assigned to the same Homologous Superfamily, but each domain has a distinct colour.

ted image 2

Other important examples to better understand the complexity of protein architectures:

SPR protein (AF-A0A836E5A2-F1), this entry contains one domain with insertions between segments, resulting in three boundaries, according to TED data. This illustrates how a single domain can have discontinuous segments in the sequence.

ted image 3

Inosine-5'-monophosphate dehydrogenase (AF-Q21KQ8-F1) here, where a split domain (Domain 1, green) has another domain (Domain 2, orange) nested between its segments. This demonstrates the complexity of domain architectures compared to sequence.

ted image 4

In the help section How to interpret the Predicted Aligned Error, we discussed the multi-domain protein like Disco-interacting protein 2 homolog B (AF-Q9P265-F1). With the integration of TED data, we see that the PAE shows a high confidence in the relative positions of domain 5 and domain 3.

ted image 5

In the DUF5621 domain-containing protein (AF-Q5ZSU4-F1), TED identifies distinct domains, and the PAE shows an overall high confidence in the relative position of all domains.

ted image 6

Some entries might not contain TED domains, such as the TrpR gene coding for the trp operon repressor protein (AF-A0A376RRE1-F1). There are several reasons why an entry might not have any TED domains, including the structural element does not qualify as a distinct domain according to TED's criteria, the fragment might not contain a complete domain or the overall entry has a very low pLDDT.

ted image 7
 


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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