S100 Family: 2.40.240.10.1.1.1.1

Representative domain: 1dfuP00

Classification Lineage (2.40.240.10.1.1.1.1)

CATH Code	Level Description	Links
2	Mainly Beta
2.40	Beta Barrel
2.40.240	Ribosomal Protein L25; Chain P
2.40.240.10	Ribosomal Protein L25; Chain P	Gene3D
2.40.240.10.1
2.40.240.10.1.1
2.40.240.10.1.1.1
2.40.240.10.1.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	31

Non-Redundant Representatives (31)
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 Count Entries in S100 Family 2.40.240.10.1.1.1.1 (31)

CATH code	Domain ID	Keywords
2.40.240.10.1.1.1.1.1	1dfuP00	Escherichia coli K-12, protein binding, large subunit ribosomal protein L25, 50S ribosomal protein L25, Ribosome
2.40.240.10.1.1.1.1.2	3i1nV00	Ribosome, Escherichia coli K-12, protein binding, large subunit ribosomal protein L25, 50S ribosomal protein L25
2.40.240.10.1.1.1.1.3	3i1pV00	50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12, Ribosome
2.40.240.10.1.1.1.1.4	2qamV00	Ribosome, large subunit ribosomal protein L25, 50S ribosomal protein L25, Escherichia coli K-12, protein binding
2.40.240.10.1.1.1.1.5	2qaoV00	protein binding, Escherichia coli K-12, 50S ribosomal protein L25, large subunit ribosomal protein L25, Ribosome
2.40.240.10.1.1.1.1.6	2i2tV00	Ribosome, 50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12
2.40.240.10.1.1.1.1.7	2i2vV00	Ribosome, large subunit ribosomal protein L25, 50S ribosomal protein L25, Escherichia coli K-12, protein binding
2.40.240.10.1.1.1.1.8	2qbeV00	Ribosome, large subunit ribosomal protein L25, 50S ribosomal protein L25, Escherichia coli K-12, protein binding
2.40.240.10.1.1.1.1.9	2qbgV00	50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12, Ribosome
2.40.240.10.1.1.1.1.10	1vs6V00	Ribosome, 50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12
2.40.240.10.1.1.1.1.11	1vs8V00	Ribosome, Escherichia coli K-12, protein binding, large subunit ribosomal protein L25, 50S ribosomal protein L25
2.40.240.10.1.1.1.1.12	2aw4V00	50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12, Ribosome
2.40.240.10.1.1.1.1.13	2awbV00	large subunit ribosomal protein L25, 50S ribosomal protein L25, Escherichia coli K-12, protein binding, Ribosome
2.40.240.10.1.1.1.1.14	2qozV00	Ribosome, Escherichia coli K-12, protein binding, large subunit ribosomal protein L25, 50S ribosomal protein L25
2.40.240.10.1.1.1.1.15	2qp1V00	Escherichia coli K-12, protein binding, large subunit ribosomal protein L25, 50S ribosomal protein L25, Ribosome
2.40.240.10.1.1.1.1.16	3df2V00	50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12, Ribosome
2.40.240.10.1.1.1.1.17	3df4V00	Ribosome, large subunit ribosomal protein L25, 50S ribosomal protein L25, Escherichia coli K-12, protein binding
2.40.240.10.1.1.1.1.18	2qbaV00	protein binding, Escherichia coli K-12, 50S ribosomal protein L25, large subunit ribosomal protein L25, Ribosome
2.40.240.10.1.1.1.1.19	2qbcV00	50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12, Ribosome
2.40.240.10.1.1.1.1.20	3i20V00	Ribosome, Escherichia coli K-12, protein binding, large subunit ribosomal protein L25, 50S ribosomal protein L25
2.40.240.10.1.1.1.1.21	3i22V00	Ribosome, 50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12
2.40.240.10.1.1.1.1.22	2vhmV00	50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12, Ribosome
2.40.240.10.1.1.1.1.23	2vhnV00	50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12, Ribosome
2.40.240.10.1.1.1.1.24	3i1rV00	Ribosome, 50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12
2.40.240.10.1.1.1.1.25	3i1tV00	Ribosome, Escherichia coli K-12, protein binding, large subunit ribosomal protein L25, 50S ribosomal protein L25
2.40.240.10.1.1.1.1.26	2qovV00	50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12, Ribosome
2.40.240.10.1.1.1.1.27	2qoxV00	Ribosome, 50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12
2.40.240.10.1.1.1.1.28	2qbiV00	Ribosome, Escherichia coli K-12, protein binding, large subunit ribosomal protein L25, 50S ribosomal protein L25
2.40.240.10.1.1.1.1.29	2qbkV00	large subunit ribosomal protein L25, 50S ribosomal protein L25, Escherichia coli K-12, protein binding, Ribosome
2.40.240.10.1.1.1.1.30	1b75A00	protein binding, Escherichia coli K-12, 50S ribosomal protein L25, large subunit ribosomal protein L25, Ribosome
2.40.240.10.1.1.1.1.31	1d6kA00	Ribosome, 50S ribosomal protein L25, large subunit ribosomal protein L25, protein binding, Escherichia coli K-12

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=2.40.240.10.1.1.1.1

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).

S100 Family: 2.40.240.10.1.1.1.1

Classification Lineage (2.40.240.10.1.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 2.40.240.10.1.1.1.1 (31)

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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