S95 Family: 3.40.50.880.2.2.1

Representative domain: 2rk3A00

Classification Lineage (3.40.50.880.2.2.1)

CATH Code	Level Description	Links
3	Alpha Beta
3.40	3-Layer(aba) Sandwich
3.40.50	Rossmann fold
3.40.50.880		Gene3D
3.40.50.880.2
3.40.50.880.2.2
3.40.50.880.2.2.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	35	45

Non-Redundant Representatives (35)
Functional Families
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What is a Non-Redundant Representative?

CATH is a tree-like organisation of nodes that begins with the class node (i.e. the first branch-point of the tree) and ends with the domain nodes (i.e. the leaves of the tree). Each node below the class have a parent that they belong to, e.g. the parent of the H level (Homologous superfamily) is the T (Topology). Additionally, each node above the domains have child nodes that belong to them, e.g. the child nodes of a given H (Homologous superfamily) level are the S35 families (domains clustered at > 35% sequence identity).

S100 Family Entries in S95 Family 3.40.50.880.2.2.1 (35)

CATH code	Representative Domain	Representative Keywords	Number of Domains
3.40.50.880.2.2.1.1	2rk3A00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Homo sapiens	1
3.40.50.880.2.2.1.2	1p5fA00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Protein DJ-1	9
3.40.50.880.2.2.1.3	2rk4A00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Protein DJ-1	1
3.40.50.880.2.2.1.4	3cz9A00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.5	3ezgA00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.6	2rk6A00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.7	1soaA00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.8	3czaA00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.9	3f71A00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.10	3cy6A00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Protein DJ-1	1
3.40.50.880.2.2.1.11	3b36A00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.12	3b3aA00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.13	3cyfA00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.14	1pe0A00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Protein DJ-1	2
3.40.50.880.2.2.1.15	2r1tA00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Homo sapiens	2
3.40.50.880.2.2.1.16	2r1tB00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.17	2r1vB00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Protein DJ-1	1
3.40.50.880.2.2.1.18	3b38A00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.19	1pdvA00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.20	1pdwG00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.21	1pdwE00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.22	1pdwA00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.23	1pdwB00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.24	1pdwC00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Homo sapiens	1
3.40.50.880.2.2.1.25	1pdwD00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.26	1pdwF00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Protein DJ-1	1
3.40.50.880.2.2.1.27	1pdwH00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Homo sapiens	1
3.40.50.880.2.2.1.28	3bweE00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.29	3bweA00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.30	3bweB00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.31	3bweC00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein DJ-1Protein DJ-1	1
3.40.50.880.2.2.1.32	3bweD00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.33	3bweF00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.34	3bweG00	Regulation of androgen receptor signaling pathwayParkinson's diseaseNucleusProtein bindingNegative regulation of protein binding	1
3.40.50.880.2.2.1.35	1j42A00	Parkinson's diseaseRegulation of androgen receptor signaling pathwayNucleusProtein bindingNegative regulation of protein binding	1

The information on Functional Families (FunFams) is currently being updated and will be released by the end of March 2012. The pages will include the following features:

Multiple alignments for each functional family
Representative structure for each functional with known catalytic and interface residues highlighted, along with conserved residues predicted by scorecons
Detailed functional information on diversity and conservation within Functional families
Multi-domain architectures

In the meantime, please find a summary of information on the FunFams and protein networks within this superfamily on the Gene3D pages:

http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=3.40.50.880.2.2.1

What is a Non-Redundant Representative?

Why can't I have a multiple structural alignment of the whole superfamily?

The simple answer is that some of the larger superfamilies in CATH comprise relatives which are very structurally diverse, having different secondary structure embellishments. Attempting to provide a global alignment of all domains in the superfamily would result in poor quality alignments. As a result, structural alignments in CATH are generated by first clustering together the structures that have at least some recognisable structural similarity using a normalised RMSD score (SIMAX = RMSDxNumber of residues in the largest domain/number of aligned residues) less than a given cutoff.

What is an Close Structural Cluster?

A Close Structural Cluster describes a cluster of two or more CATH domains that have been grouped together due to their close structural similarity (SIMAX score < 5Å where SIMAX = RMSD x Number of residues in the larger domain/number of aligned residues).

What is a Distant Structural Cluster?

A Distant Structural Cluster describes a cluster of two or CATH domains that have been grouped together with a more relaxed structural similarity threshold to investigate more distant evolutionary similarities (SIMAX score < 5Å where SIMAX = RMSD x Number of residues in the larger domain/number of aligned residues).

What is a Structural Neighbour?

The term "structural neighbour" is used here to describe two CATH domains that share a degree of structural similarity. The SSAP algorithm is used to calculate this similarity and works by generating a structure-based pairwise alignment of the two domains then scoring this alignment using a RMSD score which has been normalised by the length of the larger domain divided by the number of aligned residues (SIMAX).

S95 Family: 3.40.50.880.2.2.1

Classification Lineage (3.40.50.880.2.2.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Family Entries in S95 Family 3.40.50.880.2.2.1 (35)

What is a Non-Redundant Representative?

Why can't I have a multiple structural alignment of the whole superfamily?

What is an Close Structural Cluster?

What is a Distant Structural Cluster?

What is a Structural Neighbour?

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