S95 Family: 3.40.50.2000.1.1.1

Representative domain: 2gj4A02

Classification Lineage (3.40.50.2000.1.1.1)

CATH Code	Level Description	Links
3	Alpha Beta
3.40	3-Layer(aba) Sandwich
3.40.50	Rossmann fold
3.40.50.2000	Glycogen Phosphorylase B;	Gene3D
3.40.50.2000.1
3.40.50.2000.1.1
3.40.50.2000.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	56	165

Non-Redundant Representatives (56)
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 3.40.50.2000.1.1.1 (56)

CATH code	Representative Domain	Representative Keywords	Number of Domains
3.40.50.2000.1.1.1.1	2gj4A02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	105
3.40.50.2000.1.1.1.2	1a8iA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.3	2qnbA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.4	2qrqA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.5	2qrhA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.6	2qrgA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.7	2qrpA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.8	2pyiA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.9	2qrmA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.10	3eboA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.11	2pydA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.12	3cuvA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.13	2qn3A02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.14	2gpnA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.15	3bcsA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.16	3bd6A02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.17	3cuwA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.18	3ebpA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.19	3g2iA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.20	3g2kA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.21	1z6qA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.22	3bcuA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.23	3g2hA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.24	2g9rA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.25	2qlmA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.26	3g2nA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.27	3bcrA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.28	3g2jA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.29	2g9uA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.30	2g9vA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.31	2qlnA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.32	2offA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.33	3cutA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.34	3cuuA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.35	3g2lA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.36	1nojA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	6
3.40.50.2000.1.1.1.37	1z6pA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.38	2qn1A02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.39	2g9qA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.40	3e3lA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.41	3e3lB02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.42	3e3lC02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.43	3e3lD02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.44	3e3oA02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.45	3e3oB02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.46	3e3oC02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.47	3e3oD02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.48	2qn2A02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.49	3e3nA02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.50	3e3nB02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.51	3e3nC02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.52	3e3nD02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.53	3e3nE02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.54	3e3nF02	Glycogen phosphorylase, muscle formPhosphorylase.Oryctolagus cuniculus	1
3.40.50.2000.1.1.1.55	3e3nG02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	1
3.40.50.2000.1.1.1.56	3e3nH02	Phosphorylase.Glycogen phosphorylase, muscle formOryctolagus cuniculus	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=3.40.50.2000.1.1.1

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).

S95 Family: 3.40.50.2000.1.1.1

Classification Lineage (3.40.50.2000.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Family Entries in S95 Family 3.40.50.2000.1.1.1 (56)

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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