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Probable G-protein coupled receptor 85

Reviewed
Reference proteome

AF-P60894-F1-v4

DownloadPDB file mmCIF file Predicted aligned error

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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.

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SequenceNo structure available
Structure Tools
  • 20:51:44
    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
050100150200250300350050100150200250300350
  • 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.
PDB ID
and chain
DescriptionSpecies Residue
range
E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
Seq.
identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
Res.
(Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
Align
in 3D
Align in 3D
PDB ID and
chain
2y00_B_1
Description

Beta-1 adrenergic receptor

Beta-1 adrenergic receptor

Species

Meleagris gallopavo

Meleagris gallopavo

Residue range

33 - 368P07700

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
6.36e-11
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
18.8%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.50
Align in 3D
PDB ID and
chain
7e32_R_5
Description

Soluble cytochrome b562

5-hydroxytryptamine receptor 1D

Soluble cytochrome b562

5-hydroxytryptamine recepto...

5-hydroxytryptamine receptor 1D
Species

Escherichia coli

Homo sapiens

Escherichia coli

Homo sapiens

Residue range

23 - 128P0ABE7

2 - 377P28221

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
8.67e-11
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
18.1%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.90
Align in 3D
PDB ID and
chain
7vgy_A_1
Description

Melatonin receptor type 1A

Melatonin receptor type 1A

Species

Homo sapiens

Homo sapiens

Residue range

1 - 350P48039

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
9.90e-11
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
18.4%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.10
Align in 3D
PDB ID and
chain
2y01_B_1
Description

Beta-1 adrenergic receptor

Beta-1 adrenergic receptor

Species

Meleagris gallopavo

Meleagris gallopavo

Residue range

33 - 368P07700

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
1.08e-10
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
18.5%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.60
Align in 3D
PDB ID and
chain
2ycw_B_1
Description

Beta-1 adrenergic receptor

Beta-1 adrenergic receptor

Species

Meleagris gallopavo

Meleagris gallopavo

Residue range

33 - 367P07700

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
1.48e-10
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
18.9%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.00
Align in 3D
PDB ID and
chain
2y03_A_1
Description

Beta-1 adrenergic receptor

Beta-1 adrenergic receptor

Species

Meleagris gallopavo

Meleagris gallopavo

Residue range

33 - 368P07700

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
1.61e-10
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
18.9%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.85
Align in 3D
PDB ID and
chain
6kuw_A_1
Description

Alpha-2C adrenergic receptor

Alpha-2C adrenergic receptor

Starch synthase catalytic domain-containing protein

Alpha-2C adrenergic recepto...

Alpha-2C adrenergic receptor

Alpha-2C adrenergic recepto...

Alpha-2C adrenergic receptor

Starch synthase catalytic d...

Starch synthase catalytic domain-containing protein
Species

Homo sapiens

Homo sapiens

Pyrococcus abyssi (strain GE5 / Orsay)

Homo sapiens

Homo sapiens

Pyrococcus abyssi (strain G...

Pyrococcus abyssi (strain GE5 / Orsay)
Residue range

29 - 241P18825

372 - 458P18825

218 - 413Q9V2J8

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
1.93e-10
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
16.3%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.80
Align in 3D
PDB ID and
chain
2y02_B_1
Description

Beta-1 adrenergic receptor

Beta-1 adrenergic receptor

Species

Meleagris gallopavo

Meleagris gallopavo

Residue range

33 - 368P07700

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
2.10e-10
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
18.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.60
Align in 3D
PDB ID and
chain
8hn1_A_2
Description

Alpha-1A adrenergic receptor

Alpha-1A adrenergic receptor

Alpha-1A adrenergic recepto...

Alpha-1A adrenergic receptor

Alpha-1A adrenergic recepto...

Alpha-1A adrenergic receptor
Species

Homo sapiens

Homo sapiens

Homo sapiens

Homo sapiens

Residue range

1 - 268P35348

269 - 371P35348

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
2.30e-10
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
18.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.90
Align in 3D
PDB ID and
chain
2y03_B_1
Description

Beta-1 adrenergic receptor

Beta-1 adrenergic receptor

Species

Meleagris gallopavo

Meleagris gallopavo

Residue range

33 - 368P07700

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
2.40e-10
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
19.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.85
Items per page:
1 – 10 of 754
AF-P60894-F1
Current entry

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Aligned in 3D
Rotate and zoom structures in the 3D
viewer. Structures are aligned using alpha
carbon atoms as reference points. Once
aligned, RMSD values will appear in the
list below; lower values indicate greater
similarity between the two structures.
Toggle structures in both PDB and AFDB tables to view and align them with the entry structure in the 3D viewer. You can also download the aligned coordinates of the toggled structures and the entry structure.
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-A0A6V7TSW3-F1
Unreviewed
Reference proteome
Description Serpentine receptor class gamma
Serpentine receptor class gamma
SpeciesMeloidogyne enterolobii
Meloidogyne enterolobii
Sequence length 339 Average pLDDT 88.44
AFDB accessionAF-A0A6V7TQW5-F1
Unreviewed
Reference proteome
Description Serpentine receptor class gamma
Serpentine receptor class gamma
SpeciesMeloidogyne enterolobii
Meloidogyne enterolobii
Sequence length 339 Average pLDDT 88.06
AFDB accessionAF-A0A6V7WFB1-F1
Unreviewed
Reference proteome
Description Serpentine receptor class gamma
Serpentine receptor class gamma
SpeciesMeloidogyne enterolobii
Meloidogyne enterolobii
Sequence length 339 Average pLDDT 87.56
AFDB accessionAF-A0A1Y2BDA3-F1
Unreviewed
Reference proteome
Description Family A G protein-coupled receptor-like protein

Family A G protein-coupled receptor-like protein ...

Family A G protein-coupled receptor-like protein
SpeciesRhizoclosmatium globosum
Rhizoclosmatium globosum
Sequence length 342 Average pLDDT 84.75
AFDB accessionAF-A0A2C9KQ59-F1
Unreviewed
Reference proteome
Description G_PROTEIN_RECEP_F1_2 domain-containing protein

G_PROTEIN_RECEP_F1_2 domain-containing protein ...

G_PROTEIN_RECEP_F1_2 domain-containing protein
SpeciesBiomphalaria glabrata
Biomphalaria glabrata
Sequence length 354 Average pLDDT 84.38
AFDB accessionAF-P60895-F1
Reviewed (Swiss-Prot)
Reference proteome
Description Probable G-protein coupled receptor 85

Probable G-protein coupled receptor 85 ...

Probable G-protein coupled receptor 85
SpeciesRattus norvegicus
Rattus norvegicus
Sequence length 370 Average pLDDT 83.05
AFDB accessionAF-A0A813M4G1-F1
Unreviewed
Reference proteome
Description Hypothetical protein
Hypothetical protein
SpeciesBrachionus calyciflorus
Brachionus calyciflorus
Sequence length 396 Average pLDDT 83
AFDB accessionAF-P60894-F1
Reviewed (Swiss-Prot)
Reference proteome
Description Probable G-protein coupled receptor 85

Probable G-protein coupled receptor 85 ...

Probable G-protein coupled receptor 85
SpeciesMus musculus
Mus musculus
Sequence length 370 Average pLDDT 82.96
AFDB accessionAF-Q9I919-F1
Reviewed (Swiss-Prot)
Reference proteome
Description Probable G protein-coupled receptor 85

Probable G protein-coupled receptor 85 ...

Probable G protein-coupled receptor 85
SpeciesDanio rerio
Danio rerio
Sequence length 371 Average pLDDT 82.49
AFDB accessionAF-Q5E9H8-F1
Reviewed (Swiss-Prot)
Reference proteome
Description Probable G-protein coupled receptor 173

Probable G-protein coupled receptor 173 ...

Probable G-protein coupled receptor 173
SpeciesBos taurus
Bos taurus
Sequence length 373 Average pLDDT 82.48
Items per page:
1 – 10 of 4791

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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