S100 Family: 3.10.450.40.2.1.1.1

Representative domain: 2oqeB01

Classification Lineage (3.10.450.40.2.1.1.1)

CATH Code	Level Description	Links
3	Alpha Beta
3.10	Roll
3.10.450	Nuclear Transport Factor 2; Chain: A,
3.10.450.40		Gene3D
3.10.450.40.2
3.10.450.40.2.1
3.10.450.40.2.1.1
3.10.450.40.2.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	21

Non-Redundant Representatives (21)
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 3.10.450.40.2.1.1.1 (21)

CATH code	Domain ID	Keywords
3.10.450.40.2.1.1.1.1	2oqeB01	Peroxisomal primary amine oxidase, Pichia angusta, Primary-amine oxidase.
3.10.450.40.2.1.1.1.2	2oqeE01	Peroxisomal primary amine oxidase, Pichia angusta, Primary-amine oxidase.
3.10.450.40.2.1.1.1.3	2oqeA01	Primary-amine oxidase., Pichia angusta, Peroxisomal primary amine oxidase
3.10.450.40.2.1.1.1.4	2oqeC01	Primary-amine oxidase., Peroxisomal primary amine oxidase, Pichia angusta
3.10.450.40.2.1.1.1.5	2oqeD01	Primary-amine oxidase., Peroxisomal primary amine oxidase, Pichia angusta
3.10.450.40.2.1.1.1.6	2oqeF01	Primary-amine oxidase., Pichia angusta, Peroxisomal primary amine oxidase
3.10.450.40.2.1.1.1.7	2oovA01	Pichia angusta, Peroxisomal primary amine oxidase, Primary-amine oxidase.
3.10.450.40.2.1.1.1.8	2oovB01	Peroxisomal primary amine oxidase, Pichia angusta, Primary-amine oxidase.
3.10.450.40.2.1.1.1.9	2oovC01	Primary-amine oxidase., Pichia angusta, Peroxisomal primary amine oxidase
3.10.450.40.2.1.1.1.10	2oovD01	Peroxisomal primary amine oxidase, Pichia angusta, Primary-amine oxidase.
3.10.450.40.2.1.1.1.11	2oovE01	Peroxisomal primary amine oxidase, Pichia angusta, Primary-amine oxidase.
3.10.450.40.2.1.1.1.12	2oovF01	Peroxisomal primary amine oxidase, Pichia angusta, Primary-amine oxidase.
3.10.450.40.2.1.1.1.13	1a2vA01	Peroxisomal primary amine oxidase, Pichia angusta, Primary-amine oxidase.
3.10.450.40.2.1.1.1.14	1a2vB01	Primary-amine oxidase., Pichia angusta, Peroxisomal primary amine oxidase
3.10.450.40.2.1.1.1.15	1a2vC01	Primary-amine oxidase., Peroxisomal primary amine oxidase, Pichia angusta
3.10.450.40.2.1.1.1.16	1a2vD01	Primary-amine oxidase., Pichia angusta, Peroxisomal primary amine oxidase
3.10.450.40.2.1.1.1.17	1a2vE01	Pichia angusta, Peroxisomal primary amine oxidase, Primary-amine oxidase.
3.10.450.40.2.1.1.1.18	1a2vF01	Primary-amine oxidase., Pichia angusta, Peroxisomal primary amine oxidase
3.10.450.40.2.1.1.1.19	1ekmA01	Primary-amine oxidase., Pichia angusta, Peroxisomal primary amine oxidase
3.10.450.40.2.1.1.1.20	1ekmB01	Peroxisomal primary amine oxidase, Pichia angusta, Primary-amine oxidase.
3.10.450.40.2.1.1.1.21	1ekmC01	Primary-amine oxidase., Pichia angusta, Peroxisomal primary amine oxidase

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=3.10.450.40.2.1.1.1

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: 3.10.450.40.2.1.1.1

Classification Lineage (3.10.450.40.2.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 3.10.450.40.2.1.1.1 (21)

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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