S100 Family: 3.30.420.10.13.1.1.1

Representative domain: 2zd1A05

Classification Lineage (3.30.420.10.13.1.1.1)

CATH Code	Level Description	Links
3	Alpha Beta
3.30	2-Layer Sandwich
3.30.420	Nucleotidyltransferase; domain 5
3.30.420.10		Gene3D
3.30.420.10.13
3.30.420.10.13.1
3.30.420.10.13.1.1
3.30.420.10.13.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	50

Non-Redundant Representatives (50)
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 3.30.420.10.13.1.1.1 (50)

CATH code	Domain ID	Keywords
3.30.420.10.13.1.1.1.1	2zd1A05	HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Retroviral ribonuclease H., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10
3.30.420.10.13.1.1.1.2	3dlkA05	Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Retroviral ribonuclease H., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.3	3k2pA00	HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Retroviral ribonuclease H., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.4	3k2pB00	Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.5	3bgrA05	Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.6	2be2A05	RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Retroviral ribonuclease H., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.7	3is9A05	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein
3.30.420.10.13.1.1.1.8	2iajA05	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein
3.30.420.10.13.1.1.1.9	2b6aA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Retroviral ribonuclease H.
3.30.420.10.13.1.1.1.10	1s9eA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Retroviral ribonuclease H.
3.30.420.10.13.1.1.1.11	1dloA05	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein
3.30.420.10.13.1.1.1.12	1hquA05	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Retroviral ribonuclease H.
3.30.420.10.13.1.1.1.13	1hqeA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein
3.30.420.10.13.1.1.1.14	1hniA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin.
3.30.420.10.13.1.1.1.15	2hmiA05	Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10
3.30.420.10.13.1.1.1.16	1r0aA05	Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10
3.30.420.10.13.1.1.1.17	2vg5A05	Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Retroviral ribonuclease H., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10
3.30.420.10.13.1.1.1.18	3ig1A05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Retroviral ribonuclease H.
3.30.420.10.13.1.1.1.19	3irxA05	RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, Retroviral ribonuclease H., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.20	1qe1A05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.21	2vg7A05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.22	1tvrA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Retroviral ribonuclease H.
3.30.420.10.13.1.1.1.23	2ic3A05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.24	1hnvA05	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, Retroviral ribonuclease H., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.25	1s6pA05	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein
3.30.420.10.13.1.1.1.26	1sv5A05	RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, Retroviral ribonuclease H., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.27	2b5jA05	HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Retroviral ribonuclease H., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10
3.30.420.10.13.1.1.1.28	2ze2A05	Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.29	1hpzA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Retroviral ribonuclease H.
3.30.420.10.13.1.1.1.30	1n6qA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein
3.30.420.10.13.1.1.1.31	2banA05	RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Retroviral ribonuclease H., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.32	1t05A05	Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.33	3jsmA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin.
3.30.420.10.13.1.1.1.34	1hysA05	Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10
3.30.420.10.13.1.1.1.35	1s9gA05	HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Retroviral ribonuclease H., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10
3.30.420.10.13.1.1.1.36	1s6qA05	Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Retroviral ribonuclease H., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10
3.30.420.10.13.1.1.1.37	1suqA05	Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.38	1bqmA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin.
3.30.420.10.13.1.1.1.39	1n5yA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin.
3.30.420.10.13.1.1.1.40	1t03A05	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., Retroviral ribonuclease H.
3.30.420.10.13.1.1.1.41	2vg6A05	Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10
3.30.420.10.13.1.1.1.42	1uwbA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin.
3.30.420.10.13.1.1.1.43	1tv6A05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Retroviral ribonuclease H., RNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin.
3.30.420.10.13.1.1.1.44	2i5jA05	Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.45	1hmvA05	HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Retroviral ribonuclease H., DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10
3.30.420.10.13.1.1.1.46	1hmvC05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Retroviral ribonuclease H.
3.30.420.10.13.1.1.1.47	1hmvE05	Retroviral ribonuclease H., Gag-Pol polyprotein, HIV-1 retropepsin., RNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase.
3.30.420.10.13.1.1.1.48	1hmvG05	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, Retroviral ribonuclease H., RNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein
3.30.420.10.13.1.1.1.49	3jytA05	DNA-directed DNA polymerase., Human immunodeficiency virus type 1 BH10, HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Retroviral ribonuclease H.
3.30.420.10.13.1.1.1.50	1j5oA05	Human immunodeficiency virus type 1 BH10, DNA-directed DNA polymerase., HIV-1 retropepsin., Gag-Pol polyprotein, RNA-directed DNA polymerase., Retroviral ribonuclease H.

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=3.30.420.10.13.1.1.1

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: 3.30.420.10.13.1.1.1

Classification Lineage (3.30.420.10.13.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 3.30.420.10.13.1.1.1 (50)

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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