CATH Domain: 2rgrA05

2rgrA05

PDB 2rgr, Chain A, Domain 5

CATH Code	Level Description	Links
1	Mainly Alpha
1.10	Orthogonal Bundle
1.10.268	Topoisomerase; domain 3
1.10.268.10	Topoisomerase, domain 3	Gene3D
1.10.268.10.2
1.10.268.10.2.1
1.10.268.10.2.1.1
1.10.268.10.2.1.1.1
1.10.268.10.2.1.1.1.2

Structure
Sequence
History

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Segment boundaries for domain 2rgrA05

Domain	Start PDB Residue	Stop PDB Residue
2rgrA01	429	561
2rgrA01	609	691
2rgrA02	562	608
2rgrA03	692	860
2rgrA03	974	988
2rgrA04	872	973
2rgrA05	989	1177

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).

Structural Neighbourhood (5 entries)

There are 5 matching structural neighberhood comparisons for CATH ID 1.10.268.10.2.1.1.1.2 (SIMAX score < 5)

Match	SSAP score	Match Keywords	Match Superfamily	Length	Sequence Id	Overlap	RMSD	SIMAX
1bjtA03	89.40	Reciprocal meiotic recombinationRegulation of mitotic recombinationDNA topoisomerase 2DNA topoisomerase II [EC:5.99.1.3]DNA strand elongation involved in DNA replication	1.10.268.10	106	99	68	0.48	0.70
1bgwA03	88.96	Reciprocal meiotic recombinationRegulation of mitotic recombinationDNA topoisomerase 2DNA topoisomerase II [EC:5.99.1.3]DNA strand elongation involved in DNA replication	1.10.268.10	110	95	68	0.60	0.87
3b5nA00	67.82	Synaptobrevin homolog 1Vesicle fusionSNAP receptor activityPlasma membraneVesicle-associated membrane protein 4	1.20.5.110	61	1	25	0.61	2.39
1ci6B00	66.45	Mammary gland epithelial cell differentiationMammary gland epithelial cell proliferationCytoplasmProtein heterodimerization activitySequence-specific enhancer binding RNA polymerase II transcription factor activity	1.20.5.170	47	2	26	1.08	4.03
2o1kA00	66.37	Simian rotavirus A/SA11-bothNon-structural glycoprotein 4	1.20.5.430	42	11	27	1.34	4.88

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Domain ATOM Sequence

>pdb|2rgrA05
SVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYY
GSLYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR

BLAST against CATH

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Domain COMBS Sequence

>pdb|2rgrA05
SVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYY
GSLYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR

BLAST against CATH

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Domain History Events (101)

Domain assigned by cuff on 21 Jan 2009 13:27

homology match

Domain assignment manual match h by cuff on 21 Jan 2009 13:26

same superfamily

Homcheck allotment by cuff on 21 Jan 2009 13:25

User 'cuff' has allocated a domain to themselves for HomChecking with comment : Grabbed this domain via HomCheck's "Get Me A Domain" button.

Flow stage update by cuff on 21 Jan 2009 13:25

User 'cuff' has allocated a domain to themselves for HomChecking with comment : Grabbed this domain via HomCheck's "Get Me A Domain" button.

Flow stage update by auto on 06 Nov 2008 00:36

Domain "2rgrA05" SCOP scan with no results - no SCOP mapping

Domain scan scop cath by auto on 06 Nov 2008 00:35

Adding scan of type "DOMAIN_SCAN_SCOP_CATH" with 0 results for 2rgrA05

Flow stage update by auto on 06 Nov 2008 00:26

Retrieved PRC_PFAMCATH results for job ID SID1876930655457376 and results inserted.

Domain scan prc pfamcath by auto on 06 Nov 2008 00:25

Adding scan of type "DOMAIN_SCAN_PRC_PFAMCATH" with 11 results for 2rgrA05

Update comment by auto on 05 Nov 2008 20:52

PRC_PFAMCATH job SID1876930655457376 is not yet finished.

Flow stage update by auto on 05 Nov 2008 20:49

The entry "2rgrA05" has been submitted to the PRC_PFAMCATH webservice.

Prc pfamcath submit by auto on 05 Nov 2008 20:49

The entry "2rgrA05" has been submitted to the PRC_PFAMCATH webservice.

Flow stage update by auto on 05 Nov 2008 20:31

Retrieved SSAP results for job ID SID7834483591084992 and results inserted.

Domain scan ssap cath by auto on 05 Nov 2008 20:29

Adding scan of type "DOMAIN_SCAN_SSAP_CATH" with 1579 results for 2rgrA05

Update comment by auto on 03 Nov 2008 17:50

SSAP job SID7834483591084992 is not yet finished.

Flow stage update by auto on 03 Nov 2008 17:38

The entry "2rgrA05" has been submitted to the SSAP webservice.

Ssap cath submit by auto on 03 Nov 2008 17:38

The entry "2rgrA05" has been submitted to the SSAP webservice.

Flow stage update by auto on 03 Nov 2008 14:35

Giving up on SSAP job SID1191781119413088 because submission time of Tue Oct 28 12:16:10 2008 is more than 518400 seconds older than current time (Mon Nov 3 14:35:01 2008).

Update comment by auto on 28 Oct 2008 12:34

SSAP job SID1191781119413088 is not yet finished.

Flow stage update by auto on 28 Oct 2008 12:16

The entry "2rgrA05" has been submitted to the SSAP webservice.

Ssap cath submit by auto on 28 Oct 2008 12:16

The entry "2rgrA05" has been submitted to the SSAP webservice.

Flow stage update by auto on 28 Oct 2008 08:59

Giving up on SSAP job SID2710602035932096 because submission time of Wed Oct 22 09:29:13 2008 is more than 518400 seconds older than current time (Tue Oct 28 08:59:24 2008).

Update comment by auto on 22 Oct 2008 09:44

SSAP job SID2710602035932096 is not yet finished.

Ssap cath submit by auto on 22 Oct 2008 09:29

The entry "2rgrA05" has been submitted to the SSAP webservice.

Flow stage update by auto on 22 Oct 2008 09:29

The entry "2rgrA05" has been submitted to the SSAP webservice.

Flow stage update by auto on 22 Oct 2008 06:25

Giving up on SSAP job SID9361423157114408 because submission time of Thu Oct 16 06:06:32 2008 is more than 518400 seconds older than current time (Wed Oct 22 06:25:37 2008).

Update comment by auto on 16 Oct 2008 06:23

SSAP job SID9361423157114408 is not yet finished.

Ssap cath submit by auto on 16 Oct 2008 06:06

The entry "2rgrA05" has been submitted to the SSAP webservice.

Flow stage update by auto on 16 Oct 2008 06:06

The entry "2rgrA05" has been submitted to the SSAP webservice.

Flow stage update by auto on 16 Oct 2008 03:36

Giving up on SSAP job SID5593292960133312 because submission time of Fri Oct 10 03:09:52 2008 is more than 518400 seconds older than current time (Thu Oct 16 03:36:10 2008).

Update comment by auto on 10 Oct 2008 03:45

SSAP job SID5593292960133312 is not yet finished.

Ssap cath submit by auto on 10 Oct 2008 03:09

The entry "2rgrA05" has been submitted to the SSAP webservice.

Flow stage update by auto on 10 Oct 2008 03:09

The entry "2rgrA05" has been submitted to the SSAP webservice.

Flow stage update by auto on 10 Oct 2008 02:02

Retrieved PRC results for job ID SID8984241369143440 and inserted them into the database.

Domain scan prc cath by auto on 10 Oct 2008 02:02

Adding scan of type "DOMAIN_SCAN_PRC_CATH" with 3 results for 2rgrA05

Update comment by auto on 09 Oct 2008 06:50

PRC job SID8984241369143440 is not yet finished.

Prc cath submit by auto on 09 Oct 2008 06:21

The entry "2rgrA05" has been submitted to the PRC webservice.

Flow stage update by auto on 09 Oct 2008 06:21

The entry "2rgrA05" has been submitted to the PRC webservice.

Flow stage update by auto on 09 Oct 2008 05:55

Retrieved HMM(SAM) results for job ID SID8006443879418448 and inserted them into the database.

Domain scan sam cath by auto on 09 Oct 2008 05:55

Adding scan of type "DOMAIN_SCAN_SAM_CATH" with 3 results for 2rgrA05