SUPERFAMILY 1.75 HMM library and genome assignments server

PKD domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Immunoglobulin-like beta-sandwich [ 48725] (28)
Superfamily:   PKD domain [ 49299]
Families:   PKD domain [ 49300] (3)

Superfamily statistics
Genomes (868) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 6,995 11,242 3
Proteins 3,415 6,245 3

Functional annotation
General category General
Detailed category General

Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism cellular process 0.09886 Least Informative Inherited
Biological Process (BP) biological adhesion 5.973e-08 Informative Direct
Biological Process (BP) cell adhesion 2.898e-08 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) anion binding 0.0043 Moderately Informative Inherited
Molecular Function (MF) receptor binding 0.0007256 Informative Direct
Molecular Function (MF) carbohydrate derivative binding 2.643e-07 Informative Direct
Molecular Function (MF) sulfur compound binding 7.852e-08 Informative Direct
Molecular Function (MF) heparin binding 6.659e-09 Highly Informative Direct
Molecular Function (MF) protein complex binding 2.741e-06 Highly Informative Direct
Cellular Component (CC) membrane 0.0004396 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.06858 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.7515 Least Informative Inherited
Cellular Component (CC) vesicle 7.851e-09 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.0008895 Moderately Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details) Document: EC annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.0001573Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentMembrane8.879e-14Least InformativeDirect
Cellular componentEndosome1.396e-08Moderately InformativeDirect
Cellular componentGolgi apparatus1.062e-06Moderately InformativeDirect
DomainSignal3.01e-14Least InformativeDirect
DomainTransmembrane8.844e-09Least InformativeDirect
DomainRepeat8.453e-05Least InformativeDirect
Post-translational modificationGlycoprotein4.74e-11Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000601 SSF49299 Protein matches

The PKD domain was first identified in the Polycystic kidney disease protein, polycystin-1 (PDK1 gene), and contains an Ig-like fold consisting of a beta-sandwich of seven strands in two sheets with a Greek key topology, although some members have additional strands [PubMed9889186]. Polycystin-1 is a large cell-surface glycoprotein involved in adhesive protein-protein and protein-carbohydrate interactions; however it is not clear if the PKD domain mediates any of these interactions.

PKD domains are also found in other proteins, usually in the extracellular parts of proteins involved in interactions with other proteins. For example, domains with a PKD-type fold are found in archaeal surface layer proteins that protect the cell from extreme environments [PubMed12377130], and in the human VPS10 domain-containing receptor SorCS2 [PubMed11499680].

InterPro database

PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 3 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.

Browse and view proteins in genomes which have different domain combinations including a PKD domain domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.

Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 3 hidden Markov models representing the PKD domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]