CATH Domain: 3b40A01

3b40A01

PDB 3b40, Chain A, Domain 1

CATH Code	Level Description	Links
3	Alpha Beta
3.20	Alpha-Beta Barrel
3.20.20	TIM Barrel
3.20.20.140	Metal-dependent hydrolases	Gene3D
3.20.20.140.16
3.20.20.140.16.1
3.20.20.140.16.1.1
3.20.20.140.16.1.1.1
3.20.20.140.16.1.1.1.1

Structure
Sequence
History

[top]
Segment boundaries for domain 3b40A01

Domain	Start PDB Residue	Stop PDB Residue
3b40A01	38	304
3b40A01	363	442
3b40A02	305	362

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 (3 entries)

There are 3 matching structural neighberhood comparisons for CATH ID 3.20.20.140.16.1.1.1.1 (SIMAX score < 5)

Match	SSAP score	Match Keywords	Match Superfamily	Length	Sequence Id	Overlap	RMSD	SIMAX
2ragA00	88.73	Caulobacter vibrioidesDipeptidase	3.20.20.140	369	32	88	2.06	2.34
1ituA00	86.83	Membrane dipeptidase [EC:3.4.13.19]Homo sapiensDipeptidase 1Metalloexopeptidase activityProtein binding	3.20.20.140	369	23	89	2.16	2.42
2i5gA00	85.58	Pseudomonas aeruginosaPutative uncharacterized protein	3.20.20.140	317	23	85	2.03	2.38

[top]
Domain ATOM Sequence

>pdb|3b40A01
YPRKVMQHAEELHERILSFDSRITVPLDFGTTGNEVDKDGPGQLDLVKAGRGRLSGAALAIFGWPEMWPHKPTPGFVDEA
RHQQEIRYKILTGMVRDFPNQVGIAYSPEDFRRLAMEGKFAIVMSMLNAYPLGDDLSQLDKWAARGVRMFGFSYVGNNDW
ADSSRPLPFFNDSPDALGGLSPLGKQAVERLNDLGVIIDVSQMSTKALEQVAALSRAPIVASHSAPRALVDIKRNLSDHE
MQLIKDSGGVIQVVGFPAYLRPKAGLKELVDAIDYTVKKVGIDHVGISSDFNDGGGVDGWKDVSEIRNVTAELITRGYSD
ADIAKLWGGNFLRAWGEVQKRA

BLAST against CATH

[top]
Domain COMBS Sequence

>pdb|3b40A01
SLSEAGYPRKVMQHAEELHERILSFDSRITVPLDFGTTGNEVDKDGPGQLDLVKAGRGRLSGAALAIFGWPEMWNGPNAP
HKPTPGFVDEARHQQEIRYKILTGMVRDFPNQVGIAYSPEDFRRLAMEGKFAIVMSMLNAYPLGDDLSQLDKWAARGVRM
FGFSYVGNNDWADSSRPLPFFNDSPDALGGLSPLGKQAVERLNDLGVIIDVSQMSTKALEQVAALSRAPIVASHSAPRAL
VDIKRNLSDHEMQLIKDSGGVIQVVGFPAYLRPKAGLKELVDAIDYTVKKVGIDHVGISSDFNDGGGVDGWKDVSEIRNV
TAELITRGYSDADIAKLWGGNFLRAWGEVQKRAKPTATP

BLAST against CATH

[top]
Domain History Events (45)

Domain assigned by cuff on 23 Jan 2009 14:38

homology match

Domain assignment manual match h by cuff on 23 Jan 2009 14:37

same superfamily

Homcheck allotment by cuff on 23 Jan 2009 14:35

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 23 Jan 2009 14:35

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 28 Oct 2008 19:13

Domain "3b40A01" SCOP scan with no results - no SCOP mapping

Domain scan scop cath by auto on 28 Oct 2008 19:13

Adding scan of type "DOMAIN_SCAN_SCOP_CATH" with 0 results for 3b40A01

Flow stage update by auto on 28 Oct 2008 18:41

Retrieved PRC_PFAMCATH results for job ID SID0980802398092136 and results inserted.

Domain scan prc pfamcath by auto on 28 Oct 2008 18:41

Adding scan of type "DOMAIN_SCAN_PRC_PFAMCATH" with 23 results for 3b40A01

Update comment by auto on 27 Oct 2008 03:54

PRC_PFAMCATH job SID0980802398092136 is not yet finished.

Flow stage update by auto on 27 Oct 2008 03:51

The entry "3b40A01" has been submitted to the PRC_PFAMCATH webservice.

Prc pfamcath submit by auto on 27 Oct 2008 03:51

The entry "3b40A01" has been submitted to the PRC_PFAMCATH webservice.

Flow stage update by auto on 27 Oct 2008 03:19

Retrieved SSAP results for job ID SID3969080149358082 and results inserted.

Domain scan ssap cath by auto on 27 Oct 2008 03:17

Adding scan of type "DOMAIN_SCAN_SSAP_CATH" with 308 results for 3b40A01

Update comment by auto on 23 Oct 2008 18:40

SSAP job SID3969080149358082 is not yet finished.

Ssap cath submit by auto on 23 Oct 2008 18:20

The entry "3b40A01" has been submitted to the SSAP webservice.

Flow stage update by auto on 23 Oct 2008 18:20

The entry "3b40A01" has been submitted to the SSAP webservice.

Flow stage update by auto on 23 Oct 2008 17:48

Retrieved PRC results for job ID SID7900517669850496 and inserted them into the database.

Domain scan prc cath by auto on 23 Oct 2008 17:48

Adding scan of type "DOMAIN_SCAN_PRC_CATH" with 8 results for 3b40A01

Update comment by auto on 23 Oct 2008 10:09

PRC job SID7900517669850496 is not yet finished.

Flow stage update by auto on 23 Oct 2008 10:04

The entry "3b40A01" has been submitted to the PRC webservice.

Prc cath submit by auto on 23 Oct 2008 10:04

The entry "3b40A01" has been submitted to the PRC webservice.

Flow stage update by auto on 23 Oct 2008 09:45

Retrieved HMM(SAM) results for job ID SID6685203776324224 and inserted them into the database.

Domain scan sam cath by auto on 23 Oct 2008 09:45

Adding scan of type "DOMAIN_SCAN_SAM_CATH" with 5 results for 3b40A01

Update comment by auto on 22 Oct 2008 17:45

HMM(SAM) job SID6685203776324224 is not yet finished.

Flow stage update by auto on 22 Oct 2008 17:44

The entry "3b40A01" has been submitted to the HMM (SAM) webservice.

Sam cath submit by auto on 22 Oct 2008 17:44

The entry "3b40A01" has been submitted to the HMM (SAM) webservice.

Flow stage update by auto on 22 Oct 2008 17:34

Retrieved "3b40A01" CATHEDRAL results for job ID SID8738178117354872 and inserted them into the database.

Domain scan cathedral cath by auto on 22 Oct 2008 17:33

Adding scan of type "DOMAIN_SCAN_CATHEDRAL_CATH" with 142 results for 3b40A01

Update comment by auto on 22 Oct 2008 14:40

"3b40A01" CATHEDRAL job SID8738178117354872 is not yet finished.

Cathedral cath submit by auto on 22 Oct 2008 14:32

The entry "3b40A01" has been submitted to the CATHEDRAL webservice.

Flow stage update by auto on 22 Oct 2008 14:32

The entry "3b40A01" has been submitted to the CATHEDRAL webservice.

Flow stage update by auto on 22 Oct 2008 14:17

ScanList with 12259 domains written to "/cath/data/current/scanlists/cathdb_current.fletcher/3b40A01.scanlist" for "3b40A01"

Write scan list by auto on 22 Oct 2008 14:17

Writing ScanList containing 12259 domains to file "/cath/data/current/scanlists/cathdb_current.fletcher/3b40A01.scanlist" for domain "3b40A01"

Update comment by auto on 22 Oct 2008 11:51

Waiting for 14 new domains (example : 3dgvA01) to be processed so that they can be scanned against too.

Update comment by auto on 22 Oct 2008 09:11

Waiting for 42 new domains (example : 3cb5B01) to be processed so that they can be scanned against too.

Update comment by auto on 22 Oct 2008 06:02

Waiting for 73 new domains (example : 3bjeA01) to be processed so that they can be scanned against too.

Update comment by auto on 22 Oct 2008 01:58

Waiting for 121 new domains (example : 3bgaA05) to be processed so that they can be scanned against too.

Update comment by auto on 21 Oct 2008 20:35

Waiting for 174 new domains (example : 3beeB00) to be processed so that they can be scanned against too.

Update comment by auto on 21 Oct 2008 18:33

Waiting for 225 new domains (example : 3b8sB01) to be processed so that they can be scanned against too.

Flow stage update by auto on 21 Oct 2008 17:25

No satisfactory AssignClose result found.

Flow stage update by auto on 21 Oct 2008 17:08

No in_process hits for Domain "3b40A01" ready to be processed

Flow stage update by auto on 21 Oct 2008 17:07

NW result present for Domain "3b40A01"

Flow stage update by auto on 21 Oct 2008 08:34

All required files are present for Domain "3b40A01"

Flow stage update by auto on 20 Oct 2008 18:49

Beginning processing for Domain "3b40A01"

Insertion by cuff on 20 Oct 2008 16:24

nice chopping