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Tubulin beta-2 chain

Reviewed
Reference proteome

AF-P52275-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
  • 9:50:25
    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
01002003004000100200300400
  • 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
6dpw_H_2
Description

Tubulin beta chain

Tubulin beta chain

Species

Sus scrofa

Sus scrofa

Residue range

1 - 445P02554

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.
4.91e-73
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
91.6%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.50
Align in 3D
PDB ID and
chain
8clg_D_2
Description

Tubulin beta-2B chain

Tubulin beta-2B chain

Species

Bos taurus

Bos taurus

Residue range

1 - 431Q6B856

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.
5.18e-73
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
91.1%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.80
Align in 3D
PDB ID and
chain
6dpu_H_2
Description

Tubulin beta chain

Tubulin beta chain

Species

Sus scrofa

Sus scrofa

Residue range

1 - 445P02554

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.
5.78e-73
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
91.5%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.10
Align in 3D
PDB ID and
chain
6dpu_G_2
Description

Tubulin beta chain

Tubulin beta chain

Species

Sus scrofa

Sus scrofa

Residue range

1 - 445P02554

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.
6.82e-73
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
91.5%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.10
Align in 3D
PDB ID and
chain
6dpu_I_2
Description

Tubulin beta chain

Tubulin beta chain

Species

Sus scrofa

Sus scrofa

Residue range

1 - 445P02554

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.
6.82e-73
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
91.5%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.10
Align in 3D
PDB ID and
chain
6dpv_B_2
Description

Tubulin beta chain

Tubulin beta chain

Species

Sus scrofa

Sus scrofa

Residue range

1 - 445P02554

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.
8.04e-73
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
91.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.30
Align in 3D
PDB ID and
chain
6dpv_D_2
Description

Tubulin beta chain

Tubulin beta chain

Species

Sus scrofa

Sus scrofa

Residue range

1 - 445P02554

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.
8.04e-73
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
91.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.30
Align in 3D
PDB ID and
chain
6dpv_F_2
Description

Tubulin beta chain

Tubulin beta chain

Species

Sus scrofa

Sus scrofa

Residue range

1 - 445P02554

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.
8.04e-73
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
91.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.30
Align in 3D
PDB ID and
chain
6dpw_B_2
Description

Tubulin beta chain

Tubulin beta chain

Species

Sus scrofa

Sus scrofa

Residue range

1 - 445P02554

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.
8.49e-73
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
91.6%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.50
Align in 3D
PDB ID and
chain
6dpw_D_2
Description

Tubulin beta chain

Tubulin beta chain

Species

Sus scrofa

Sus scrofa

Residue range

1 - 445P02554

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.
8.49e-73
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
91.6%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.50
Items per page:
1 – 10 of 948
AF-P52275-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-A0A2Z2MEZ8-F1
Unreviewed
Reference proteome
Description Tubulin-like protein CetZ
Tubulin-like protein CetZ
SpeciesThermococcus profundus
Thermococcus profundus
Sequence length 364 Average pLDDT 93.75
AFDB accessionAF-A0A0X1KKQ3-F1
Unreviewed
Reference proteome
Description Tubulin-like protein CetZ
Tubulin-like protein CetZ
SpeciesThermococcus guaymasensis DSM 11113
Thermococcus guaymasensis DSM 11113
Sequence length 365 Average pLDDT 93.69
AFDB accessionAF-O59060-F1
Reviewed (Swiss-Prot)
Reference proteome
Description Tubulin-like protein CetZ
Tubulin-like protein CetZ
SpeciesPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)...

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Sequence length 365 Average pLDDT 93.66
AFDB accessionAF-Q8U0S7-F1
Reviewed (Swiss-Prot)
Reference proteome
Description Tubulin-like protein CetZ
Tubulin-like protein CetZ
SpeciesPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)...

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Sequence length 366 Average pLDDT 93.45
AFDB accessionAF-B7R048-F1
Unreviewed
Reference proteome
Description Tubulin-like protein CetZ
Tubulin-like protein CetZ
SpeciesThermococcus sp. AM4
Thermococcus sp. AM4
Sequence length 365 Average pLDDT 93.44
AFDB accessionAF-A0A075LR88-F1
Unreviewed
Reference proteome
Description Tubulin-like protein CetZ
Tubulin-like protein CetZ
SpeciesPalaeococcus pacificus DY20341
Palaeococcus pacificus DY20341
Sequence length 363 Average pLDDT 93.38
AFDB accessionAF-Q24829-F1
Reviewed (Swiss-Prot)
Description Tubulin beta chain
Tubulin beta chain
SpeciesEncephalitozoon hellem
Encephalitozoon hellem
Sequence length 439 Average pLDDT 93.32
AFDB accessionAF-A0A429GNE1-F1
Unreviewed
Reference proteome
Description Tubulin domain-containing protein
Tubulin domain-containing protein
SpeciesCandidatus Methanodesulfokores washburnensis

Candidatus Methanodesulfokores washburnensis...

Candidatus Methanodesulfokores washburnensis
Sequence length 393 Average pLDDT 93.31
AFDB accessionAF-C5A4W3-F1
Unreviewed
Reference proteome
Description Tubulin-like protein CetZ
Tubulin-like protein CetZ
SpeciesThermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)

Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)...

Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)
Sequence length 365 Average pLDDT 93.19
AFDB accessionAF-W0I5E9-F1
Unreviewed
Reference proteome
Description Tubulin-like protein CetZ
Tubulin-like protein CetZ
SpeciesThermococcus paralvinellae
Thermococcus paralvinellae
Sequence length 364 Average pLDDT 93.19
Items per page:
1 – 10 of 13519

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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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).
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Cheng, J et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science (2023).

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