CATH Domain: 1gdtB02 XML data for domain: 1gdtB02

Molscript image for 1gdtB02
1gdtB02
PDB coordinates for domain 1gdtB02

PDB 1gdt, Chain B, Domain 2

CATH CodeLevel DescriptionLinks
1 Mainly Alpha
1.20 Up-down Bundle
1.20.5 Single alpha-helices involved in coiled-coils or other helix-helix interfaces
1.20.5.40 Gene3D
1.20.5.40.1
1.20.5.40.1.1
1.20.5.40.1.1.1
1.20.5.40.1.1.1.1
1.20.5.40.1.1.1.1.1

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Segment boundaries for domain 1gdtB02

Chopping figure for domain 1gdtB02
DomainStart PDB ResidueStop PDB Residue
1gdtB01 1 98
1gdtB02 99 138
1gdtB03 139 183

Structural Neighbourhood (116 entries)

There are 116 matching structural neighberhood comparisons for CATH ID 1.20.5.40.1.1.1.1.1 (SIMAX score < 5)

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Displaying entries 1 to 116 (page 1 of 1)
Match Depth Match SSAP score Match Keywords Match Superfamily Length Sequence Id Overlap RMSD SIMAX
1tiiC00 90.31 Heat-labile enterotoxin IIB, A chainEscherichia coli 1.20.5.200 36 11 90 1.72 1.91
1g2cB00 89.96 Human respiratory syncytial virus strain RSS-2Fusion glycoprotein F0 1.20.5.170 40 5 92 2.41 2.61
2h8pD00 89.44 1.20.5.110 43 2 93 3.87 4.16
1czqA00 89.21 1.20.5.170 45 15 88 2.37 2.67
1nkzB00 89.19 Rhodoblastus acidophilusLight-harvesting protein B-800/850 beta chain 1.20.5.250 41 7 92 3.16 3.41
2p7jB01 88.88 Vibrio parahaemolyticusPutative sensory box/GGDEF family protein 1.20.5.170 39 5 92 2.32 2.51
1s5lX00 88.27 Photosystem II reaction center X proteinThermosynechococcus elongatus BP-1 1.20.5.510 40 2 95 3.27 3.44
1a2xB00 88.03 Troponin I, fast skeletal muscleTroponin T bindingOryctolagus cuniculus 1.20.5.420 31 3 77 0.94 1.21
3effK02 87.81 Streptomyces lividansVoltage-gated potassium channel 1.20.5.440 45 12 84 2.34 2.77
1afoA00 87.78 Glycophorin-AIdentical protein bindingMembrane fractionPlasma membraneHomo sapiens 1.20.5.70 40 12 92 3.67 3.97
1hf9A00 87.62 Protein homodimerization activityNegative regulation of hydrolase activityATPase inhibitor activityBos taurusATPase binding 1.20.5.500 41 0 85 2.25 2.64
1jekA00 87.17 Visna/maedi virus EV1 KV1772Envelope glycoprotein gp160 1.20.5.440 40 17 72 1.54 2.12
1m56D00 87.16 Rhodobacter sphaeroidesAa3-type cytochrome c oxidase subunit IV 1.20.5.160 42 2 80 2.48 3.06
2k9jB00 86.82 Positive regulation of endothelial cell migrationPlatelet-derived growth factor receptor bindingPositive regulation of endothelial cell proliferationActivation of protein kinase activityRegulation of bone resorption 1.20.5.100 43 17 81 2.22 2.73
3gg2A02 86.50 Amino sugar and nucleotide sugar metabolismStarch and sucrose metabolismPentose and glucuronate interconversionsSugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase familyUDPglucose 6-dehydrogenase [EC:1.1.1.22] 1.20.5.100 32 9 80 1.60 2.00
2basA02 86.30 Bacillus subtilisUncharacterized EAL-domain containing protein ykuI 1.20.5.170 46 2 86 3.11 3.58
2k1aA00 86.21 Integrin alpha 2BIdentical protein bindingPathways in cancerHematopoietic cell lineageDilated cardiomyopathy 1.20.5.930 42 5 95 4.27 4.48
1fzcB03 86.19 Chaperone bindingSoluble fractionFibrinogen complexEukaryotic cell surface bindingFibrinogen beta chain 1.20.5.50 51 10 78 2.93 3.74
1dp5B00 85.92 CytoplasmProtease A inhibitor 3Saccharomyces cerevisiaeVacuolar protein catabolic processProtein binding 1.20.5.140 31 6 75 1.61 2.15
2v7qJ00 85.88 Protein homodimerization activityNegative regulation of hydrolase activityATPase inhibitor activityBos taurusCalmodulin binding 1.20.5.500 43 5 86 3.41 3.96
1n2dC00 85.64 Mating projection tipGolgi inheritanceActin filament bindingVesicle-mediated transportMyosin-2 1.20.5.190 48 15 75 2.25 3.00
1kv4A00 85.60 Moricin-1Bombyx mori 1.20.5.750 42 5 88 2.45 2.78
1ik7A00 85.59 Regulation of proteolysisProtein domain specific bindingHemocyte proliferationPlasma membraneZygotic specification of dorsal/ventral axis 1.20.5.530 52 12 76 2.93 3.81
2zxeB01 85.49 1.20.5.170 35 5 77 2.23 2.88
3efgA00 85.48 Xanthomonas campestris pv. campestrisSlyX proteinProtein slyX homolog 1.20.5.300 49 10 77 2.55 3.29
1ci6A00 85.30 Positive regulation of transcription from RNA polymerase II promoterCellular amino acid metabolic processNeurotrophin signaling pathwayActivating transcription factor 4Sequence-specific DNA binding transcription factor activity 1.20.5.170 56 5 71 2.58 3.61
1ybkA00 85.26 TetrabrachionStaphylothermus marinus 1.20.5.1060 52 7 76 2.21 2.87
1jmmA01 85.15 Major cell-surface adhesin PAcStreptococcus mutans 1.20.5.250 32 9 72 1.84 2.54
1ci6B00 85.07 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 7 82 2.16 2.60
2qjyB02 85.01 Rhodobacter sphaeroidesCytochrome c1 1.20.5.100 35 14 72 1.64 2.26
1go9A00 84.91 1.20.5.480 39 12 85 2.36 2.78
1hj0A00 84.86 Bos taurusThymosin beta-10 1.20.5.520 41 7 87 3.67 4.18
1kilE00 84.84 Complexin-1Syntaxin-1 bindingRattus norvegicusDendriteSynaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex 1.20.5.580 41 7 75 2.49 3.29
1ifpA00 84.80 Pseudomonas phage Pf3Capsid protein G8P 1.20.5.440 44 2 90 3.54 3.89
2zjsE00 84.76 Protein exportBacterial secretion systemThermus thermophilus HB8Preprotein translocase subunit secEPreprotein translocase subunit SecE 1.20.5.1030 46 7 78 2.22 2.84
1slqF02 84.72 Outer capsid protein VP4Rhesus rotavirus 1.20.5.170 32 0 80 3.32 4.15
2qjpB02 84.65 Rhodobacter sphaeroidesCytochrome c1 1.20.5.100 35 14 72 1.70 2.34
2qjyC01 84.53 Oxidative phosphorylationMetabolic pathwaysRhodobacter sphaeroidesUbiquinol-cytochrome c reductase iron-sulfur subunitUbiquinol-cytochrome c reductase iron-sulfur subunit [EC:1.10.2.2] 1.20.5.510 33 12 82 1.94 2.35
3kpeA00 84.33 Fusion glycoprotein F0Human respiratory syncytial virus A2 1.20.5.300 47 0 80 2.64 3.27
1jcdB00 84.32 Peptidoglycan bindingMurein lipoproteinMajor outer membrane lipoprotein LppProtein bindingEscherichia coli K-12 1.20.5.190 52 10 76 2.94 3.82
3e7kA00 83.89 Rattus norvegicusCalcium channel activityCalcium ion transportIntegral to membraneProtein binding 1.20.5.1010 54 7 74 3.14 4.24
1m7lA00 83.89 Negative regulation of T cell proliferationProtein bindingInnate immune responseLung alveolus developmentEndocytic vesicle 1.20.5.360 40 12 72 2.05 2.83
2pjuD03 83.88 Positive regulation of gene-specific transcriptionPropionate catabolism operon regulatory proteinNegative regulation of gene-specific transcriptionEscherichia coli K-12Specific transcriptional repressor activity 1.20.5.170 41 7 80 3.98 4.94
2o1kA00 83.84 Simian rotavirus A/SA11-bothNon-structural glycoprotein 4 1.20.5.430 42 10 69 3.14 4.55
1dh3A00 83.57 Positive regulation of multicellular organism growthLactationRegulation of cell sizeAxonogenesisMus musculus 1.20.5.170 55 7 69 1.68 2.43
1gmjD00 83.43 Negative regulation of hydrolase activityProtein homodimerization activityATPase inhibitor activityBos taurusCalmodulin binding 1.20.5.500 56 7 66 2.48 3.75
1gl2A00 83.25 Rattus norvegicusProtein complex assemblyVesicle-associated membrane protein 8Cellular membrane fusionVesicle-associated membrane protein 8 1.20.5.110 53 15 75 3.13 4.15
1u57A00 83.22 Human immunodeficiency virus type 1 lw12.3 isolateGag polyprotein 1.20.5.760 48 12 83 2.84 3.41
1xrdA01 82.68 Light-harvesting complex 1 alpha chainRhodospirillum rubrumLight-harvesting protein B-870 alpha chain 1.20.5.890 43 7 88 3.22 3.64
2r44A01 82.60 Cytophaga hutchinsonii ATCC 33406MoxR-like ATPase [EC:3.6.3.-]Putative uncharacterized protein 1.20.5.420 26 11 65 1.20 1.85
3b8eB00 82.53 Sodium/potassium-transporting ATPase subunit beta-1Sus scrofa 1.20.5.170 46 2 86 4.24 4.88
1kqfB03 82.52 Two-component systemMetabolic pathwaysGlyoxylate and dicarboxylate metabolismMethane metabolismFormate dehydrogenase activity 1.20.5.480 44 5 90 4.03 4.43
1jnmA00 82.51 Pathways in cancerChagas diseaseNeurotrophin signaling pathwayB cell receptor signaling pathwayT cell receptor signaling pathway 1.20.5.170 56 15 69 1.84 2.64
2c0wA00 82.42 Enterobacteria phage fdCapsid protein G8P 1.20.5.80 50 12 80 2.60 3.25
1kmiZ01 82.37 Bacterial chemotaxisChemotaxis protein cheZProtein bindingChemotaxis protein CheZEscherichia coli K-12 1.20.5.590 30 0 75 3.51 4.68
1nhlA00 82.36 Vesicle targetingAzurophil granuleCellular membrane fusionSynaptosomal-associated protein 23Protein binding 1.20.5.110 52 2 69 2.23 3.22
1vf5C03 81.97 Mastigocladus laminosusApocytochrome f 1.20.5.700 32 3 57 1.15 2.00
1a02F00 81.80 Promoter bindingPathways in cancerChagas diseaseProto-oncogene protein c-fosB cell receptor signaling pathway 1.20.5.170 53 10 62 1.49 2.39
1vpcA00 81.79 HIV-1 M:B_89.6Protein Vpr 1.20.5.90 45 2 64 1.56 2.42
2e42A00 81.36 Transcription from RNA polymerase II promoterAcute-phase responseHomo sapiensCCAAT/enhancer-binding protein betaImmune response 1.20.5.170 65 5 61 2.55 4.14
1r8eA03 81.36 Multidrug-efflux transporter 1 regulatorBacillus subtilis 1.20.5.490 44 2 68 2.55 3.74
1omiA02 81.36 Listeria monocytogenesListeriolysin regulatory protein 1.20.5.460 27 7 65 2.84 4.37
2oarE02 81.32 Large conductance mechanosensitive channel, MscL familyLarge-conductance mechanosensitive channelMycobacterium tuberculosis H37Ra 1.20.5.220 22 4 55 1.13 2.05
2b9bA04 81.28 Simian virus 5 (strain W3)Fusion glycoprotein F0 1.20.5.1070 62 7 64 2.87 4.45
1gu4A00 81.25 Transcription from RNA polymerase II promoterAcute-phase responseHomo sapiensCCAAT/enhancer-binding protein betaImmune response 1.20.5.170 65 5 61 2.58 4.19
1l2pA00 80.99 Oxidative phosphorylationMetabolic pathwaysATP synthesis coupled proton transportAnchored to membraneF-type H+-transporting ATPase subunit b [EC:3.6.3.14] 1.20.5.620 61 12 52 1.36 2.59
1gl2B00 80.98 Mus musculusSyntaxin-7 1.20.5.110 59 5 67 3.28 4.84
1e5wA04 80.89 Leukocyte migrationReceptor bindingCytoskeletonMembrane to membrane dockingNucleolus 1.20.5.450 55 12 72 3.16 4.34
1jy2S00 80.87 Bos taurusFibrinogen gamma chainFibrinogen gamma-B chainComplement and coagulation cascades 1.20.5.50 47 2 82 4.03 4.86
1ozhA03 80.75 Acetolactate synthase, catabolicKlebsiella pneumoniae 1.20.5.740 24 20 60 1.85 3.08
1owaA01 80.67 Structural constituent of cytoskeletonSpectrinHomo sapiensSpectrin-associated cytoskeletonActin filament organization 1.20.5.170 32 15 70 2.71 3.87
3ii6A02 80.54 DNA ligation involved in DNA repairProtein C-terminus bindingDNA-dependent protein kinase-DNA ligase 4 complexResponse to X-rayDouble-strand break repair via nonhomologous end joining 1.20.5.370 58 7 68 3.04 4.41
1jocA01 80.45 Zinc ion bindingVesicle fusionMembrane fractionSynaptic vesicle to endosome fusionProtein homodimerization activity 1.20.5.390 60 7 66 2.41 3.62
1be3K00 80.20 Cardiac muscle contractionCytochrome b-c1 complex subunit 10Oxidative phosphorylationParkinson's diseaseAlzheimer's disease 1.20.5.220 22 9 55 1.08 1.96
1jy2O00 80.15 Bos taurusFibrinogen beta chain 1.20.5.50 51 5 62 2.43 3.87
1vl2A03 80.08 Thermotoga maritimaArginine and proline metabolismArgininosuccinate synthase [EC:6.3.4.5]Alanine, aspartate and glutamate metabolismArgininosuccinate synthase 1.20.5.470 32 3 80 3.82 4.78
2p10B02 80.06 Mesorhizobium lotiMll9387 protein 1.20.5.460 26 7 55 1.66 3.02
1rh5B00 79.84 Protein transport protein SEC61 subunit gamma and related proteinsProtein exportMethanocaldococcus jannaschiiPreprotein translocase subunit secE 1.20.5.820 56 7 67 2.59 3.82
1gl2D00 79.76 Syntaxin-8Rattus norvegicusProtein bindingSyntaxin 8SNARE interactions in vesicular transport 1.20.5.110 54 7 57 1.87 3.26
1ppjD01 79.73 Cardiac muscle contractionUbiquinol-cytochrome c reductase cytochrome c1 subunit [EC:1.10.2.2]Parkinson's diseaseOxidative phosphorylationAlzheimer's disease 1.20.5.100 44 7 81 3.06 3.74
1t3jA00 79.72 Mus musculusMitochondrial fusionMitofusin-1Protein binding 1.20.5.110 62 7 56 2.44 4.32
1gd2F00 79.68 NuA4 histone acetyltransferase complexFungal AP-1-like factorResponse to hydrogen peroxideResponse to methylglyoxalCellular response to oxidative stress 1.20.5.170 64 12 57 2.38 4.12
1fdoA05 79.64 Methane metabolismMetabolic pathwaysGlyoxylate and dicarboxylate metabolismFormate dehydrogenase HFormate dehydrogenase, alpha subunit [EC:1.2.1.2] 1.20.5.460 27 0 62 2.47 3.95
1s3jB01 79.55 Bacillus subtilisUncharacterized HTH-type transcriptional regulator yusO 1.20.5.420 30 10 75 3.15 4.20
2k9yA00 79.51 ApoptosisIntegral to plasma membraneEphrin type-A receptor 2Homo sapiensEph receptor A2 [EC:2.7.10.1] 1.20.5.510 41 10 73 2.58 3.53
1gk6B00 79.31 Positive regulation of RNA polymerase II transcriptional preinitiation complex assemblyIntermediate filamentVimentinCytosolPositive regulation of gene-specific transcription from RNA polymerase II promoter 1.20.5.170 52 7 59 2.73 4.58
1lwuC03 79.13 Fibrinogen gamma chainPetromyzon marinus 1.20.5.50 62 5 64 2.78 4.31
1mqsB00 78.96 Vesicle fusionSyntaxin 5SNAP receptor activityER to Golgi vesicle-mediated transportRetrograde vesicle-mediated transport, Golgi to ER 1.20.5.460 26 0 65 2.13 3.28
1pp9E01 78.92 Cytochrome b-c1 complex subunit Rieske, mitochondrialBos taurus 1.20.5.270 64 5 62 2.30 3.68
1h8bB00 78.90 TitinOryctolagus cuniculus 1.20.5.510 23 13 57 1.91 3.32
2ifoA00 78.88 Xanthomonas phage XfCapsid protein G8P 1.20.5.230 46 7 63 2.64 4.19
1pfiA00 78.82 Pseudomonas phage Pf1Capsid protein G8P 1.20.5.230 46 7 58 2.69 4.58
1gk4C00 78.69 Cellular component movementProtein C-terminus bindingIntermediate filamentVimentinCytosol 1.20.5.170 70 7 57 2.38 4.17
1urqC00 78.44 SNARE interactions in vesicular transportSleepRattus norvegicusRegulation of synaptogenesisVoltage-gated potassium channel complex 1.20.5.110 68 0 58 2.70 4.59
3cx5E01 78.27 Cytochrome b-c1 complex subunit Rieske, mitochondrialMitochondrial respiratory chain complex IIIOxidative phosphorylationMetabolic pathwaysAerobic respiration 1.20.5.270 55 10 56 2.53 4.49
1junA00 78.17 Pathways in cancerChagas diseaseNeurotrophin signaling pathwayB cell receptor signaling pathwayT cell receptor signaling pathway 1.20.5.170 43 5 62 2.84 4.52
1pl5A00 78.08 Chromatin silencing complexLoss of chromatin silencing involved in replicative cell agingChromatin silencingDouble-strand break repair via nonhomologous end joiningDouble-stranded DNA binding 1.20.5.730 75 17 48 1.54 3.21
3fwlA01 77.59 Peptidoglycan biosynthesisPenicillin-binding protein 1B [EC:2.4.1.129 3.4.-.-]Penicillin bindingPenicillin-binding protein 1BPeptidoglycan biosynthetic process 1.20.5.100 31 6 70 2.51 3.59
1wt6B00 77.55 ATP bindingProtein phosphorylationRegulation of heart contractionHomo sapiensProtein serine/threonine kinase activity 1.20.5.340 67 12 59 2.70 4.52
1n7sB00 77.46 Protein domain specific bindingActomyosinMyosin head/neck bindingRattus norvegicusProtein binding, bridging 1.20.5.110 68 5 58 2.41 4.10
1n7sA00 77.41 SNARE interactions in vesicular transportVasopressin-regulated water reabsorptionRattus norvegicusProtein complex bindingVesicle-mediated transport 1.20.5.110 63 7 61 2.57 4.15
1avyA00 77.21 Enterobacteria phage T4Fibritin 1.20.5.320 68 7 51 2.11 4.10
1svfC00 77.02 Simian virus 5 (strain W3)Fusion glycoprotein F0 1.20.5.300 62 12 56 2.51 4.45
2k37A00 76.99 Bacteriochlorophyll c-binding proteinChlorobaculum tepidumChlorosome envelope protein A 1.20.5.950 59 12 64 3.00 4.66
2wwwC01 76.26 Methylmalonic aciduria type A protein, mitochondrialHomo sapiensLAO/AO transport system kinase [EC:2.7.-.-] 1.20.5.170 52 5 50 1.69 3.38
2oarA02 76.23 Large conductance mechanosensitive channel, MscL familyLarge-conductance mechanosensitive channelMycobacterium tuberculosis H37Ra 1.20.5.220 17 11 42 0.53 1.25
1j1dB00 76.21 Response to calcium ionTroponin C bindingPositive regulation of ATPase activityActin bindingNegative regulation of ATPase activity 1.20.5.350 70 7 55 2.58 4.63
1piqA00 76.03 NucleusPositive regulation of RNA polymerase II transcriptional preinitiation complex assemblyGeneral control protein GCN4General control protein GCN4Specific RNA polymerase II transcription factor activity 1.20.5.170 31 3 55 2.73 4.96
2o01J01 75.92 Photosystem I reaction center subunit IXSpinacia oleracea 1.20.5.510 25 4 62 2.96 4.74
2i8dA02 75.21 Hypothetical proteinLactobacillus casei ATCC 334Putative uncharacterized protein 1.20.5.420 30 6 55 2.61 4.75
1vl2B03 74.81 Thermotoga maritimaArginine and proline metabolismArgininosuccinate synthase [EC:6.3.4.5]Alanine, aspartate and glutamate metabolismArgininosuccinate synthase 1.20.5.470 30 10 67 3.28 4.86
2qiwA02 72.47 Corynebacterium glutamicumPEP phosphonomutase and related enzymes 1.20.5.510 18 5 45 1.07 2.38
1d66B02 70.67 Regulatory protein GAL4NucleusSequence-specific DNA binding transcription factor activityTranscription activator activityPositive regulation of transcription by galactose 1.20.5.640 15 6 37 0.45 1.20
1n73D00 70.65 Fibrinogen alpha-1 chainPetromyzon marinus 1.20.5.50 90 7 34 1.54 4.47
1mslA02 69.43 1.20.5.220 18 11 40 1.95 4.88
1mkmA02 68.33 Thermotoga maritimaTranscriptional regulator, IclR family 1.20.5.640 14 0 35 0.57 1.63
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Displaying entries 1 to 116 (page 1 of 1)


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Domain ATOM Sequence 

>pdb|1gdtB02
TDGEMGKMVVTILSAVAQAERQRILERTNEGRQEAMAKGV
BLAST against CATH

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Domain COMBS Sequence 

>pdb|1gdtB02
TDGEMGKMVVTILSAVAQAERQRILERTNEGRQEAMAKGV
BLAST against CATH

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Domain History Events (3)

Set cath from cathlist by auto on 05 Mar 2006 18:17

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 18:17

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 16:38

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