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DNA helicase

Unreviewed

AF-B4DLD8-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
  • 15:42:01
    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
02004006008001k02004006008001k
  • 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
6ryr_W_7
Description

Chromodomain-helicase-DNA-binding protein 4

Chromodomain-helicase-DNA-binding protein 4

Chromodomain-helicase-DNA-b...

Chromodomain-helicase-DNA-binding protein 4

Chromodomain-helicase-DNA-b...

Chromodomain-helicase-DNA-binding protein 4
Species

Homo sapiens

Homo sapiens

Homo sapiens

Homo sapiens

Residue range

1 - 1200Q14839

1201 - 1912Q14839

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.
2.06e-56
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
40.5%
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
7tn2_W_7
Description

Chromo domain-containing protein 1

Chromo domain-containing pr...

Chromo domain-containing protein 1
Species

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Saccharomyces cerevisiae (s...

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Residue range

118 - 1274P32657

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.
6.85e-55
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
36.9%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.30
Align in 3D
PDB ID and
chain
6ryu_W_7
Description

Chromodomain-helicase-DNA-binding protein 4

Chromodomain-helicase-DNA-binding protein 4

Chromodomain-helicase-DNA-b...

Chromodomain-helicase-DNA-binding protein 4

Chromodomain-helicase-DNA-b...

Chromodomain-helicase-DNA-binding protein 4
Species

Homo sapiens

Homo sapiens

Homo sapiens

Homo sapiens

Residue range

1 - 1200Q14839

1201 - 1912Q14839

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.
3.37e-52
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
40.6%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
4.00
Align in 3D
PDB ID and
chain
6ryu_V_7
Description

Chromodomain-helicase-DNA-binding protein 4

Chromodomain-helicase-DNA-binding protein 4

Chromodomain-helicase-DNA-b...

Chromodomain-helicase-DNA-binding protein 4

Chromodomain-helicase-DNA-b...

Chromodomain-helicase-DNA-binding protein 4
Species

Homo sapiens

Homo sapiens

Homo sapiens

Homo sapiens

Residue range

1 - 1200Q14839

1201 - 1912Q14839

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.
3.37e-52
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
40.6%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
4.00
Align in 3D
PDB ID and
chain
7nkx_W_17
Description

Chromo domain-containing protein 1

Chromo domain-containing pr...

Chromo domain-containing protein 1
Species

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Saccharomyces cerevisiae (s...

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Residue range

1 - 1468P32657

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.
6.54e-51
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
38%
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
5o9g_W_8
Description

Chromo domain-containing protein 1

Chromo domain-containing pr...

Chromo domain-containing protein 1
Species

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Saccharomyces cerevisiae (s...

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Residue range

1 - 1468P32657

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.
3.64e-47
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
35.3%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
4.80
Align in 3D
PDB ID and
chain
6g0l_M_8
Description

Chromo domain-containing protein 1

Chromo domain-containing pr...

Chromo domain-containing protein 1
Species

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Saccharomyces cerevisiae (s...

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Residue range

1 - 1468P32657

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.
3.84e-47
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
35.4%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
10.00
Align in 3D
PDB ID and
chain
6ftx_W_9
Description

Chromo domain-containing protein 1

Chromo domain-containing pr...

Chromo domain-containing protein 1
Species

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Saccharomyces cerevisiae (s...

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Residue range

175 - 1269P32657

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.
1.14e-45
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
36.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
4.50
Align in 3D
PDB ID and
chain
6g0l_W_8
Description

Chromo domain-containing protein 1

Chromo domain-containing pr...

Chromo domain-containing protein 1
Species

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Saccharomyces cerevisiae (s...

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Residue range

1 - 1468P32657

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.
1.21e-45
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
36.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
10.00
Align in 3D
PDB ID and
chain
8kcb_K_7
Description

ATP-dependent DNA helicase DDM1

ATP-dependent DNA helicase ...

ATP-dependent DNA helicase DDM1
Species

Arabidopsis thaliana

Arabidopsis thaliana

Residue range

1 - 764Q9XFH4

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.
1.51e-41
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
42%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.17
Items per page:
1 – 10 of 815
AF-B4DLD8-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-C4RFG7-F1
Unreviewed
Reference proteome
Description SNF2/RAD54 family helicase
SNF2/RAD54 family helicase
SpeciesMicromonospora sp. (strain ATCC 39149 / NRRL 15099 / SCC 1413)

Micromonospora sp. (strain ATCC 39149 / NRRL 15099 / SCC 1413)...

Micromonospora sp. (strain ATCC 39149 / NRRL 15099 / SCC 1413)
Sequence length 929 Average pLDDT 86.44
AFDB accessionAF-A0A7D5Y6U4-F1
Unreviewed
Description ATP-dependent helicase
ATP-dependent helicase
SpeciesMicromonospora carbonacea
Micromonospora carbonacea
Sequence length 929 Average pLDDT 86.31
AFDB accessionAF-A0A7H8XIF2-F1
Unreviewed
Reference proteome
Description DEAD/DEAH box helicase
DEAD/DEAH box helicase
SpeciesMicromonospora carbonacea
Micromonospora carbonacea
Sequence length 929 Average pLDDT 86.31
AFDB accessionAF-A0A318NC22-F1
Unreviewed
Reference proteome
Description ATP-dependent helicase
ATP-dependent helicase
SpeciesMicromonospora arborensis
Micromonospora arborensis
Sequence length 929 Average pLDDT 86.31
AFDB accessionAF-A0A7L6B4U6-F1
Unreviewed
Reference proteome
Description ATP-dependent helicase
ATP-dependent helicase
SpeciesMicromonospora sp. 28ISP2-46
Micromonospora sp. 28ISP2-46
Sequence length 929 Average pLDDT 86.25
AFDB accessionAF-A0A562IDZ5-F1
Unreviewed
Reference proteome
Description SNF2 family DNA or RNA helicase
SNF2 family DNA or RNA helicase
SpeciesMicromonospora olivasterospora
Micromonospora olivasterospora
Sequence length 929 Average pLDDT 86.19
AFDB accessionAF-A0A1S8XX98-F1
Unreviewed
Reference proteome
Description ATP-dependent helicase
ATP-dependent helicase
SpeciesMicromonospora sp. Rc5
Micromonospora sp. Rc5
Sequence length 931 Average pLDDT 86.12
AFDB accessionAF-A0A4R4QZU7-F1
Unreviewed
Reference proteome
Description DEAD/DEAH box helicase
DEAD/DEAH box helicase
SpeciesMicromonospora sp. KC213
Micromonospora sp. KC213
Sequence length 929 Average pLDDT 86.12
AFDB accessionAF-A0A1C5AVQ8-F1
Unreviewed
Reference proteome
Description Superfamily II DNA or RNA helicase, SNF2 family

Superfamily II DNA or RNA helicase, SNF2 family ...

Superfamily II DNA or RNA helicase, SNF2 family
SpeciesMicromonospora carbonacea
Micromonospora carbonacea
Sequence length 929 Average pLDDT 86.12
AFDB accessionAF-A0A7W9LFS2-F1
Unreviewed
Reference proteome
Description Superfamily II DNA or RNA helicase
Superfamily II DNA or RNA helicase
SpeciesNonomuraea jabiensis
Nonomuraea jabiensis
Sequence length 913 Average pLDDT 86.12
Items per page:
1 – 10 of 10108

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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