CATH Domain: 1rkdA00

1rkdA00

PDB 1rkd, Chain A, Domain 0

CATH Code	Level Description	Links
3	Alpha Beta
3.40	3-Layer(aba) Sandwich
3.40.1190	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
3.40.1190.20		Gene3D
3.40.1190.20.7
3.40.1190.20.7.1
3.40.1190.20.7.1.1
3.40.1190.20.7.1.1.1
3.40.1190.20.7.1.1.1.1

Structure
Sequence
History

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Segment boundaries for domain 1rkdA00

Domain	Start PDB Residue	Stop PDB Residue
1rkdA00	4	309

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 (12 entries)

There are 12 matching structural neighberhood comparisons for CATH ID 3.40.1190.20.7.1.1.1.1 (SIMAX score < 5)

Match	SSAP score	Match Keywords	Match Superfamily	Length	Sequence Id	Overlap	RMSD	SIMAX
2fv7A00	89.92	Pentose phosphate pathwayRibokinaseRibokinase [EC:2.7.1.15]Homo sapiens	3.40.1190.20	308	35	98	2.69	2.73
1tyyB00	85.50	Amino sugar and nucleotide sugar metabolismStarch and sucrose metabolismFructose and mannose metabolismMetabolic pathwaysFructokinase [EC:2.7.1.4]	3.40.1190.20	292	25	88	2.96	3.34
1v1aA00	85.40	Thermus thermophilus HB82-dehydro-3-deoxygluconokinase [EC:2.7.1.45]Pentose and glucuronate interconversionsPentose phosphate pathway2-keto-3-deoxy-gluconate kinase	3.40.1190.20	301	23	92	2.22	2.39
2nwhA00	83.81	Agrobacterium tumefaciens str. C58Carbohydrate kinase	3.40.1190.20	303	22	94	3.98	4.20
2qcvA01	83.43	5-dehydro-2-deoxygluconokinase [EC:2.7.1.92]Bacillus haloduransInositol phosphate metabolismMetabolic pathways5-dehydro-2-deoxygluconokinase	3.40.1190.20	262	20	79	2.25	2.85
2afbB00	83.36	Thermotoga maritima2-dehydro-3-deoxygluconokinase [EC:2.7.1.45]Pentose phosphate pathwayPentose and glucuronate interconversions2-keto-3-deoxygluconate kinase	3.40.1190.20	319	20	90	2.86	3.15
2abqA00	83.20	Fructose 1-phosphate kinase1-phosphofructokinase [EC:2.7.1.56]Fructose and mannose metabolismBacillus halodurans	3.40.1190.20	302	18	94	3.20	3.38
1vk4A00	81.24	Thermotoga maritimaPutative uncharacterized protein	3.40.1190.20	276	14	83	2.85	3.41
2i5bA00	79.56	Thiamine metabolismBacillus subtilisPyridoxine kinasePhosphomethylpyrimidine kinase [EC:2.7.4.7]Metabolic pathways	3.40.1190.20	269	15	78	3.43	4.36
2ajrA01	79.49	Thermotoga maritima1-phosphofructokinase [EC:2.7.1.56]Fructose and mannose metabolismSugar kinase, pfkB family	3.40.1190.20	259	13	78	3.11	3.95
1ub0A00	79.40	TransferaseThiamine metabolismHydroxymethylpyrimidine kinase [EC:2.7.1.49]Phosphomethylpyrimidine kinase [EC:2.7.4.7]Metabolic pathways	3.40.1190.20	246	21	75	2.83	3.75
3bf5A01	78.09	Pentose phosphate pathwayRibokinase [EC:2.7.1.15]Thermoplasma acidophilumRibokinase related protein	3.40.1190.20	221	17	70	3.42	4.82

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Domain ATOM Sequence

>pdb|1rkdA00
AGSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLATDNID
ITPVSVIKGESTGVALIFVNGEGENVIGIHAGANAALSPALVEAQRERIANASALLMQLESPLESVMAAAKIAHQNKTIV
ALNPAPARELPDELLALVDIITPNETEAEKLTGIRVENDEDAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGF
RVQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFLDRQR

BLAST against CATH

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Domain COMBS Sequence

>pdb|1rkdA00
MQNAGSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLATD
NIDITPVSVIKGESTGVALIFVNGEGENVIGIHAGANAALSPALVEAQRERIANASALLMQLESPLESVMAAAKIAHQNK
TIVALNPAPARELPDELLALVDIITPNETEAEKLTGIRVENDEDAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRV
PGFRVQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFLDRQR

BLAST against CATH

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Domain History Events (133)

Update comment by auto on 16 Oct 2007 19:44

Around September/October 2007, this domain was renamed from "1rkd000" to "1rkdA00" as part of the work to deal with the remediation of the PDB (see http://remediation.wwpdb.org). Please see ticket:207 or wiki:Remediation on the CATH Trac system for more details.

Domain assigned by lewis on 19 Jan 2007 16:21

Assigning domain 1rkd000 to 3.40.1190.20 (as agreed with the CATH update team) after the chain has been rechopped. The reason is that the domain is very similar to an old domain (from the previous chopping) which was in 3.40.1190.20 at the time the chain was unchopped.