CATH Domain: 2pgdA01 XML data for domain: 2pgdA01

Molscript image for 2pgdA01
2pgdA01
PDB coordinates for domain 2pgdA01

PDB 2pgd, Chain A, Domain 1

CATH CodeLevel DescriptionLinks
3 Alpha Beta
3.40 3-Layer(aba) Sandwich
3.40.50 Rossmann fold
3.40.50.720 NAD(P)-binding Rossmann-like Domain Gene3D
3.40.50.720.17
3.40.50.720.17.2
3.40.50.720.17.2.1
3.40.50.720.17.2.1.1
3.40.50.720.17.2.1.1.1

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Segment boundaries for domain 2pgdA01

Chopping figure for domain 2pgdA01
DomainStart PDB ResidueStop PDB Residue
2pgdA01 1 180
2pgdA02 181 435
2pgdA03 436 473

Structural Neighbourhood (33 entries)

There are 33 matching structural neighberhood comparisons for CATH ID 3.40.50.720.17.2.1.1.1 (SIMAX score < 5)

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Displaying entries 1 to 33 (page 1 of 1)
Match Depth Match SSAP score Match Keywords Match Superfamily Length Sequence Id Overlap RMSD SIMAX
3ckyA01 86.61 Eubacterium barkeri2-hydroxymethyl glutarate dehydrogenase 3.40.50.720 163 19 88 2.12 2.39
2cvzA01 86.20 Valine, leucine and isoleucine degradationMetabolic pathwaysThermus thermophilus HB83-hydroxyisobutyrate dehydrogenase3-hydroxyisobutyrate dehydrogenase [EC:1.1.1.31] 3.40.50.720 153 25 85 1.90 2.22
1vpdA01 86.03 Glyoxylate and dicarboxylate metabolismMetabolic pathwaysSalmonella enterica subsp. enterica serovar Typhimurium2-hydroxy-3-oxopropionate reductase [EC:1.1.1.60]Tartronate semialdehyde reductase (TSAR) 3.40.50.720 154 22 84 1.92 2.28
1i36A01 82.75 Methanothermobacter thermautotrophicus str. Delta HConserved protein 3.40.50.720 159 15 86 2.45 2.85
1txgA01 82.47 Archaeoglobus fulgidusGlycerophospholipid metabolismGlycerol-3-phosphate dehydrogenase [NAD(P)+]Glycerol-3-phosphate dehydrogenase (NAD(P)+) [EC:1.1.1.94] 3.40.50.720 180 12 87 2.71 3.11
1bg6A01 82.01 Arthrobacter sp. 1COpine dehydrogenase 3.40.50.720 192 12 84 2.96 3.51
1dljA01 81.32 Amino sugar and nucleotide sugar metabolismStarch and sucrose metabolismPentose and glucuronate interconversionsAscorbate and aldarate metabolismMetabolic pathways 3.40.50.720 204 9 81 2.40 2.95
1f0yA01 80.90 Hydroxyacyl-coenzyme A dehydrogenase, mitochondrialHomo sapiens 3.40.50.720 196 8 83 3.14 3.78
2rafB01 80.71 [EC:1.-.-.-]OxidoreductaseLactobacillus plantarum 3.40.50.720 176 12 76 2.80 3.66
2rcyA01 80.67 Arginine and proline metabolismMetabolic pathwaysPlasmodium falciparum 3D7Pyrroline carboxylate reductasePyrroline-5-carboxylate reductase [EC:1.5.1.2] 3.40.50.720 148 16 77 2.69 3.46
1np3B01 80.49 Pantothenate and CoA biosynthesisMetabolic pathwaysValine, leucine and isoleucine biosynthesisKetol-acid reductoisomerasePseudomonas aeruginosa 3.40.50.720 182 11 85 3.04 3.57
2amfA01 80.47 Arginine and proline metabolismMetabolic pathwaysPutative pyrroline carboxylate reductasePyrroline-5-carboxylate reductase [EC:1.5.1.2]Streptococcus pyogenes serotype M1 3.40.50.720 148 12 80 2.55 3.17
2pv7A01 80.35 T-proteinNovobiocin biosynthesisHaemophilus influenzaePhenylalanine, tyrosine and tryptophan biosynthesisPrephenate dehydrogenase [EC:1.3.1.12] 3.40.50.720 154 16 80 3.44 4.28
2o3jB01 80.20 Caenorhabditis elegansAmino sugar and nucleotide sugar metabolismIdentical protein bindingEmbryo development ending in birth or egg hatchingMetabolic pathways 3.40.50.720 205 11 78 3.18 4.05
3d1lB01 79.93 Bacteroides fragilis NCTC 9343Putative uncharacterized protein 3.40.50.720 151 8 79 2.88 3.61
2ew2B01 79.86 2-dehydropantoate 2-reductase [EC:1.1.1.169]Pantothenate and CoA biosynthesis2-dehydropantoate 2-reductaseMetabolic pathwaysEnterococcus faecalis 3.40.50.720 174 12 85 3.53 4.13
1ks9A01 79.73 Pantothenate and CoA biosynthesisMetabolic pathways2-dehydropantoate 2-reductase [EC:1.1.1.169]2-dehydropantoate 2-reductase activityPantothenate biosynthetic process from valine 3.40.50.720 167 14 82 3.39 4.10
3c24A01 79.45 Jannaschia sp. CCS1Putative uncharacterized protein 3.40.50.720 168 9 83 3.97 4.74
1jayA00 78.61 Archaeoglobus fulgidusPutative uncharacterized protein 3.40.50.720 212 13 76 2.78 3.62
1ur5C01 78.44 Malate dehydrogenase [EC:1.1.1.37]Citrate cycle (TCA cycle)Pyruvate metabolismChloroflexus aurantiacus J-10-flMetabolic pathways 3.40.50.720 136 11 66 2.63 3.96
2qytA01 78.27 Porphyromonas gingivalis2-dehydropantoate 2-reductase 3.40.50.720 179 11 84 3.64 4.29
1o6zA02 77.91 Malate dehydrogenase [EC:1.1.1.37]Citrate cycle (TCA cycle)Pyruvate metabolismHaloarcula marismortuiMetabolic pathways 3.40.50.720 142 12 64 2.69 4.19
3d0oA01 77.45 Pyruvate metabolismPropanoate metabolismMetabolic pathwaysCysteine and methionine metabolismGlycolysis / Gluconeogenesis 3.40.50.720 143 8 65 2.78 4.22
1hyeA01 77.28 Malate dehydrogenase [EC:1.1.1.37]Citrate cycle (TCA cycle)Methanocaldococcus jannaschiiPyruvate metabolismMetabolic pathways 3.40.50.720 147 10 66 2.95 4.44
2hmtA00 76.88 Trk system potassium uptake protein TrkABacillus subtilisKtr system potassium uptake protein A 3.40.50.720 139 8 63 2.80 4.40
3hhpA01 76.63 Citrate cycle (TCA cycle)Pyruvate metabolismGlyoxylate and dicarboxylate metabolismMetabolic pathwaysMalate dehydrogenase [EC:1.1.1.37] 3.40.50.720 138 10 64 2.81 4.34
2i76A01 76.60 Thermotoga maritimaPutative uncharacterized protein 3.40.50.720 142 9 77 3.04 3.91
1hyhA01 76.47 Weissella confusaL-2-hydroxyisocaproate dehydrogenase 3.40.50.720 141 12 66 3.02 4.54
1xeaA01 76.22 Vibrio choleraeOxidoreductase, Gfo/Idh/MocA familyVirulence factor 3.40.50.720 117 3 63 2.80 4.44
1t2dA01 76.18 L-lactate dehydrogenaseCysteine and methionine metabolismGlycolysis / GluconeogenesisPyruvate metabolismPlasmodium falciparum CDC/Honduras 3.40.50.720 148 10 65 2.85 4.32
2aefA01 76.09 Methanothermobacter thermautotrophicus str. Delta HCalcium-gated potassium channel mthK 3.40.50.720 115 8 60 2.67 4.43
1qmgB01 75.11 NADPH bindingProtein homodimerization activityMagnesium ion bindingSpinacia oleraceaKetol-acid reductoisomerase, chloroplastic 3.40.50.720 216 10 71 3.43 4.81
1ydwA01 74.39 Arabidopsis thalianaUncharacterized oxidoreductase At4g09670 3.40.50.720 124 12 65 3.19 4.88
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Displaying entries 1 to 33 (page 1 of 1)


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Domain ATOM Sequence 

>pdb|2pgdA01
AQADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVLGAHSLEEMVSKLKKPRRIILLVKAGQAV
DNFIEKLVPLLDIGDIIIDGGNSEYRDTMRRCRDLKDKGILFVGSGVSGGEDGARYGPSLMPGGNKEAWPHIKAIFQGIA
AKVGTGEPCCDWVGDDGAGH
BLAST against CATH

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Domain COMBS Sequence 

>pdb|2pgdA01
AQADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVLGAHSLEEMVSKLKKPRRIILLVKAGQAV
DNFIEKLVPLLDIGDIIIDGGNSEYRDTMRRCRDLKDKGILFVGSGVSGGEDGARYGPSLMPGGNKEAWPHIKAIFQGIA
AKVGTGEPCCDWVGDDGAGH
BLAST against CATH

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Domain History Events (4)

Update comment by auto on 16 Oct 2007 19:44

Around September/October 2007, this domain was renamed from "2pgd001" to "2pgdA01" 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.

Set cath from cathlist by auto on 05 Mar 2006 19:17

This domain was assigned by cathlist2DB and was parsed from the cath list "/usr/local/cvs/source/lists/CathList"

Flow stage update by auto on 05 Mar 2006 19:17

This domain was assigned by cathlist2DB and was parsed from the cath list "/usr/local/cvs/source/lists/CathList"

Insertion by auto on 05 Mar 2006 17:55

PDB chopped based on information from the domall file "/usr/local/cvs/source/lists/CathDomall"