S100 Family: 2.40.70.10.4.1.13.1

Representative domain: 2pk6A00

Classification Lineage (2.40.70.10.4.1.13.1)

CATH Code	Level Description	Links
2	Mainly Beta
2.40	Beta Barrel
2.40.70	Cathepsin D, subunit A; domain 1
2.40.70.10	Acid Proteases	Gene3D
2.40.70.10.4
2.40.70.10.4.1
2.40.70.10.4.1.13
2.40.70.10.4.1.13.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	27

Non-Redundant Representatives (27)
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 2.40.70.10.4.1.13.1 (27)

CATH code	Domain ID	Keywords
2.40.70.10.4.1.13.1.1	2pk6A00	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Retroviral ribonuclease H.
2.40.70.10.4.1.13.1.2	2pk6B00	RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Retroviral ribonuclease H., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE)
2.40.70.10.4.1.13.1.3	3kdbA00	Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase., Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.4	3kdbB00	Retroviral ribonuclease H., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.5	3i8wA00	Retroviral ribonuclease H., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.6	3kddA00	Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin.
2.40.70.10.4.1.13.1.7	3kddB00	Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase., Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.8	2pk5A00	Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.9	2pk5B00	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Retroviral ribonuclease H.
2.40.70.10.4.1.13.1.10	1d4yA00	Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein
2.40.70.10.4.1.13.1.11	1d4yB00	Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.12	1a30A00	HIV-1 M:B_HXB2R, DNA-directed DNA polymerase., Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.13	1a30B00	DNA-directed DNA polymerase., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Retroviral ribonuclease H., HIV-1 M:B_HXB2R
2.40.70.10.4.1.13.1.14	1a8kA00	Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase., Retroviral ribonuclease H., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.15	1a8kB00	Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin.
2.40.70.10.4.1.13.1.16	1a8kD00	Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.17	1a8kE00	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Retroviral ribonuclease H.
2.40.70.10.4.1.13.1.18	1mrwA00	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, Retroviral ribonuclease H.
2.40.70.10.4.1.13.1.19	1mrwB00	Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase., Retroviral ribonuclease H., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.20	1msmA00	Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.21	1msmB00	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Retroviral ribonuclease H.
2.40.70.10.4.1.13.1.22	1ztzA00	Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.23	1ztzB00	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, Retroviral ribonuclease H.
2.40.70.10.4.1.13.1.24	3kdcA00	RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, Retroviral ribonuclease H., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE)
2.40.70.10.4.1.13.1.25	3kdcB00	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, Retroviral ribonuclease H.
2.40.70.10.4.1.13.1.26	1hpoA00	Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase., Retroviral ribonuclease H., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase.
2.40.70.10.4.1.13.1.27	1hpoB00	Retroviral ribonuclease H., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Human immunodeficiency virus type 1 (BRU ISOLATE), DNA-directed DNA polymerase.

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=2.40.70.10.4.1.13.1

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: 2.40.70.10.4.1.13.1

Classification Lineage (2.40.70.10.4.1.13.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 2.40.70.10.4.1.13.1 (27)

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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