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123  structures 7508  species 0  interactions 30755  sequences 827  architectures

Family: PDZ_6 (PF17820)

Summary: PDZ domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

PDZ domain Provide feedback

This entry represents the PDZ domain from a wide variety of proteins.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR041489

This entry represents the PDZ domain from a wide variety of proteins. It is part of the Pfam clan PDZ-like (CL0466). PDZ domains are peptide binding sites.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PDZ-like (CL0466), which has the following description:

This superfamily comprises families of PDZ domains, which are peptide binding sites.

The clan contains the following 11 members:

DUF6288 EBP50_C GRASP55_65 PDZ PDZ_1 PDZ_2 PDZ_3 PDZ_4 PDZ_5 PDZ_6 Tricorn_PDZ

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(77)
Full
(30755)
Representative proteomes UniProt
(110314)
RP15
(4804)
RP35
(14121)
RP55
(29615)
RP75
(45074)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(77)
Full
(30755)
Representative proteomes UniProt
(110314)
RP15
(4804)
RP35
(14121)
RP55
(29615)
RP75
(45074)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(77)
Full
(30755)
Representative proteomes UniProt
(110314)
RP15
(4804)
RP35
(14121)
RP55
(29615)
RP75
(45074)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: ECOD:EUF03538
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 77
Number in full: 30755
Average length of the domain: 53.40 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 7.85 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 54
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PDZ_6 domain has been found. There are 123 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0A0MPH1 View 3D Structure Click here
A0A0G2JVL3 View 3D Structure Click here
A0A0G2K212 View 3D Structure Click here
A0A0N7KSP8 View 3D Structure Click here
A0A0P0V6A3 View 3D Structure Click here
A0A0P0WIB1 View 3D Structure Click here
A0A0R0HTR5 View 3D Structure Click here
A0A0R4IAR0 View 3D Structure Click here
A0A0R4IBF0 View 3D Structure Click here
A0A0R4IVS6 View 3D Structure Click here
A0A1D6G0X9 View 3D Structure Click here
A0A1D6GMB8 View 3D Structure Click here
A0A1D6HP95 View 3D Structure Click here
A0A1D6NZN4 View 3D Structure Click here
A0A1D8PCD2 View 3D Structure Click here
A0A2R8PWV1 View 3D Structure Click here
A0A2R8PWX7 View 3D Structure Click here
A0A2R8Q0B7 View 3D Structure Click here
A0A2R8Q205 View 3D Structure Click here
A0A2R8QB42 View 3D Structure Click here
A0A2R8QBP6 View 3D Structure Click here
A0A2R8QII5 View 3D Structure Click here
A0A2R8QLZ7 View 3D Structure Click here
A0A2R8QMX6 View 3D Structure Click here
A0A2R8QN87 View 3D Structure Click here
A0A2R8QNY1 View 3D Structure Click here
A0A2R8QSQ5 View 3D Structure Click here
A0A2R8RHW5 View 3D Structure Click here
A0A2R8RHW5 View 3D Structure Click here
A0A2R8RIE2 View 3D Structure Click here
A0A2R8RTD5 View 3D Structure Click here
A0A2R8RTP4 View 3D Structure Click here
A0A2R8RTP4 View 3D Structure Click here
A0A2R8S028 View 3D Structure Click here
A0A486WTK6 View 3D Structure Click here
A1Z9K8 View 3D Structure Click here
A2RT60 View 3D Structure Click here
A4HUC6 View 3D Structure Click here
A8MUH7 View 3D Structure Click here
B0BNB9 View 3D Structure Click here
B0UYM8 View 3D Structure Click here
B0V3R3 View 3D Structure Click here
B4FYR9 View 3D Structure Click here
B6TZ03 View 3D Structure Click here
B8A617 View 3D Structure Click here
B8A620 View 3D Structure Click here
B8A623 View 3D Structure Click here
B8A632 View 3D Structure Click here
B9EJ80 View 3D Structure Click here
D3YZU1 View 3D Structure Click here
D3ZA76 View 3D Structure Click here
D3ZKF5 View 3D Structure Click here
D3ZXY2 View 3D Structure Click here
D4A7C5 View 3D Structure Click here
D4A7C5 View 3D Structure Click here
D4A7C5 View 3D Structure Click here
E1JIT7 View 3D Structure Click here
E7F723 View 3D Structure Click here
E7F765 View 3D Structure Click here
E7F7C3 View 3D Structure Click here
E7FH65 View 3D Structure Click here
E7FH65 View 3D Structure Click here
E9QBA1 View 3D Structure Click here
E9QDR9 View 3D Structure Click here
E9QEU0 View 3D Structure Click here
E9QEU2 View 3D Structure Click here
E9QFX7 View 3D Structure Click here
E9QI54 View 3D Structure Click here
F1LXQ7 View 3D Structure Click here
F1M2D4 View 3D Structure Click here
F1Q589 View 3D Structure Click here
F1Q897 View 3D Structure Click here
F1Q918 View 3D Structure Click here
F1QGZ7 View 3D Structure Click here
F1QJ05 View 3D Structure Click here
F1QL69 View 3D Structure Click here
F1QST2 View 3D Structure Click here
F1QYY8 View 3D Structure Click here
F1QZB3 View 3D Structure Click here
F1QZR5 View 3D Structure Click here
F1R0Q7 View 3D Structure Click here
F1R7L1 View 3D Structure Click here
F1RD62 View 3D Structure Click here
F4J3G5 View 3D Structure Click here
F4KHG6 View 3D Structure Click here
F6NN15 View 3D Structure Click here
F8W2C5 View 3D Structure Click here
G3XA20 View 3D Structure Click here
G5EDM4 View 3D Structure Click here
G5EDM4 View 3D Structure Click here
H9G328 View 3D Structure Click here
I1L9W8 View 3D Structure Click here
I1LRP6 View 3D Structure Click here
I1MZD3 View 3D Structure Click here
I1NBY4 View 3D Structure Click here
I1NHY3 View 3D Structure Click here
K7KQM3 View 3D Structure Click here
K7KYB8 View 3D Structure Click here
M0R3L1 View 3D Structure Click here
O00233 View 3D Structure Click here
O15021 View 3D Structure Click here
O23053 View 3D Structure Click here
O23614 View 3D Structure Click here
O43464 View 3D Structure Click here
O60307 View 3D Structure Click here
O76587 View 3D Structure Click here
P68907 View 3D Structure Click here
P97879 View 3D Structure Click here
P9WHS3 View 3D Structure Click here
Q09284 View 3D Structure Click here
Q10920 View 3D Structure Click here
Q2FYL3 View 3D Structure Click here
Q3E6S8 View 3D Structure Click here
Q3U214 View 3D Structure Click here
Q4ACU6 View 3D Structure Click here
Q4D678 View 3D Structure Click here
Q4DX34 View 3D Structure Click here
Q5T2W1 View 3D Structure Click here
Q5T5U3 View 3D Structure Click here
Q5ZA08 View 3D Structure Click here
Q60592 View 3D Structure Click here
Q69ZH9 View 3D Structure Click here
Q69ZS0 View 3D Structure Click here
Q6ASR8 View 3D Structure Click here
Q6DBR1 View 3D Structure Click here
Q6DFV3 View 3D Structure Click here
Q6P0Q8 View 3D Structure Click here
Q6TNR1 View 3D Structure Click here
Q80Z38 View 3D Structure Click here
Q810W7 View 3D Structure Click here
Q811L6 View 3D Structure Click here
Q84NY6 View 3D Structure Click here
Q86UT5 View 3D Structure Click here
Q8BWB1 View 3D Structure Click here
Q8IXQ8 View 3D Structure Click here
Q8MNT0 View 3D Structure Click here
Q8NEN9 View 3D Structure Click here
Q925T6 View 3D Structure Click here
Q92614 View 3D Structure Click here
Q92743 View 3D Structure Click here
Q93654 View 3D Structure Click here
Q99MJ6 View 3D Structure Click here
Q99MJ6 View 3D Structure Click here
Q9BYB0 View 3D Structure Click here
Q9C0E4 View 3D Structure Click here
Q9CR00 View 3D Structure Click here
Q9D236 View 3D Structure Click here
Q9EQZ7 View 3D Structure Click here
Q9JIS1 View 3D Structure Click here
Q9JIY5 View 3D Structure Click here
Q9JJ40 View 3D Structure Click here
Q9JLU4 View 3D Structure Click here
Q9P227 View 3D Structure Click here
Q9QX74 View 3D Structure Click here
Q9QZK5 View 3D Structure Click here
Q9R118 View 3D Structure Click here
Q9R1L5 View 3D Structure Click here
Q9UPX8 View 3D Structure Click here
Q9UQ26 View 3D Structure Click here
Q9VCS4 View 3D Structure Click here
Q9VFJ3 View 3D Structure Click here
Q9VFS8 View 3D Structure Click here
Q9VUQ9 View 3D Structure Click here
Q9VYR9 View 3D Structure Click here
Q9W2L2 View 3D Structure Click here
Q9WTV5 View 3D Structure Click here
Q9WTW1 View 3D Structure Click here
Q9WV48 View 3D Structure Click here
Q9Y2H9 View 3D Structure Click here
Q9Y3R0 View 3D Structure Click here
Q9Y566 View 3D Structure Click here
X1WCZ6 View 3D Structure Click here
X1WES7 View 3D Structure Click here