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PDB ID Mentions in PubMed Central Article count: 3

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PDB ID Mentions in PubMed Central

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CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships.

(2008) Genome Biol 9

PubMed: 18201387 | PubMedCentral: PMC2395249 | DOI: 10.1186/gb-2008-9-1-r11

Table 1 Retrieved parent proteins of engineered CPs by CPSARST PDB entry Chain Size Function Parent structure/recorded CP site Retrieved structure/determined CP site D (%)* 1AJK A,B 214 Circularly per... uted (1-3,1-4)-beta-D-glucan 4-glucanohydrolase H 2AYH/84 2AYH/84 0.00 1AJO A,B 214 Circularly permuted (1-3,1-4)-beta-D-glucan 4-glucanohydrolase H 2AYH/127 2AYH/127 0.00 1ALQ 266 CP254 beta-lactamase 3BLM/254 3BLM/254 0.00 1BD7 A,B 176 Circularly permuted BB2-crystallin 1BLBC/87 1BLBC/87 0.00 1CPM 214 Glucanase 2AYH/59 2AYH/59 0.00 1CPN 208 Glucanase 2AYH/59 2AYH/59 0.00 1FW8 A 416 Phosphoglycerate kinase 3PGK/72 3PGK/73 0.24 1G2B A 62 Spectrin alpha chain 1SHG/47 1SHG/47 0.00 1N02 A 102 Cyanovirin-N 2EZM/50 2EZM/51 0.98 1P5C A-D 167 Lysozyme 1LW9A/12 1LW9A/12 0.00 1SWF A-D 128 Circularly permuted core-streptavidin E51/A46 1STP/51 1STP/51 0.00 1SWG A-D 128 Circularly permuted core-streptavidin E51/A46 1STP/51 1STP/51 0.00 1TUC 63 alpha-Spectrin 1SHG/20 1SHG/20 0.00 1TUD 62 alpha-Spectrin 1SHG/48 1SHG/48 0.00 1UN2 A 197 Thiol-disulfide interchange protein 1A2J/100 1A2J/100 0.00 Average 0.08 *Percentage distance of the retrieved permutation site to the exact one.

Publication Year: 2008

What lessons can be learned from studying the folding of homologous proteins?

(2010) Methods 52

PubMed: 20570731 | PubMedCentral: PMC2965948 | DOI: 10.1016/j.ymeth.2010.06.003

Class (fold) Superfamily Protein (species) Method of investigation PDB code Experimental references Comparative references a All-α (Acyl-CoA binding protein-like) Acyl-CoA binding protein ACBP... (Cow) Φ-Value analysis 2ABD [93,94] [94] ACBP (Rat) WT kinetics 2ABD b [93] ACBP (Yeast) Φ-Value analysis 2ABD b [94] 

 All-α (Acyl carrier protein-like) Colicin E immunity proteins Im7 ( E. coli ) Φ-Value analysis 1AYI [28] [29] Im9 ( E. coli ) Φ-Value analysis 1IMQ [29,30,95] 

 All-α (Cytochrome c ) Cytochrome c Cytochrome c (Horse) Hydrogen exchange 1HRC [96] [97] Cytochrome c 2 ( R. capsulatus ) WT kinetics 1C2R [98] Cytochrome c 551 ( P. aeruginosa ) Minimal Φ-value analysis 2PAC [99] Cytochrome c 552 ( H. thermophilus ) WT kinetics 1AYG [100] Cytochrome c 552 ( T. thermophilus ) WT kinetics 1C52 [101] Mitochondrial cytochrome c (Yeast) WT kinetics 1YCC [102] 

 All-α (Four-helical up-and-down bundle) Cytochromes Cytochrome b 562 ( E. coli ) Hydrogen exchange 1APC [103] FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) FRB (Human) WT kinetics 1AUE [104] 

 All-α (DNA/RNA-binding 3-helical bundle) Homeodomain-like DNA-binding domain of human telomeric protein hTRF1 (Human) WT kinetics 1BA5 [47] [47] En-Hd (Drosophila) Φ-Value analysis 1ENH [7,105] c-Myb DNA-binding domain (Mouse) Φ-Value analysis 1IDY [47] Rap1 (Human) WT kinetics 1FEX [47] 

 All-α (Globin-like) Globin-like Leghemoglobin (Soybean) Hydrogen exchange 1FSL [106] [106] Myoglobin (Sperm whale) Hydrogen exchange 1A6M [107] 

 All-α (peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex) Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex E3 binding domain of dihydrolipoamide acetyltransferase [E3BD] ( B. stearothermophilus ) Φ-Value analysis 1EBD [58] [59] E3-binding domain of dihydrolipoamide succinyltransferase [BBL] ( E. coli ) Φ-Value analysis 1BBL [59] POB ( P. aerophilium ) Φ-Value analysis 1BBL b [60] 

 All-α (ROP-like) ROP protein ROP ( E. agglomerans ) WT kinetics 1ROP b [4] [4] ROP ( E. coli ) WT kinetics 1ROP [4] ROP ( P. vulgaris ) WT kinetics 1ROP b [4] 

 All-α (spectrin repeat-like) Spectrin repeat Alpha chain R15 (Chicken) Φ-Value analysis 1U5P [46] [46] Alpha chain R16 (Chicken) Φ-Value analysis 1CUN [81] Alpha chain R17 (Chicken) Φ-Value analysis 1CUN [45] 

 α/β (α/β knot) α/β knot YbeA ( E. coli ) Φ-Value analysis 1NS5 [108] [108] YibK ( H. influenzae ) Φ-Value analysis 1J85 [109] 

 α/β (Dihydrofolate reductase-like) Dihydrofolate reductase-like Dihydrofolate reductase ( E. coli ) WT kinetics, Ligand binding 1RA9 [110] [110] Dihyrofolate reductase ( L. casei ) WT kinetics, Ligand binding 3DFR [110] Dihydrofolate reductase (Human) WT kinetics, Ligand binding 1KMV [110] 

 α/β (flavodoxin-like) CheY-like CheY ( E. coli ) Φ-Value analysis 1EAY [111] [112] Flavoproteins Apoflavodoxin ( A. vinelandii ) WT kinetics 1YOB [113] Flavodoxin ( Anabaena pcc 7119 ) Φ-Value analysis 1FTG [112] 

 α/β (Phosphoglycerate kinase) Phosphoglycerate kinase Phosphoglycerate kinase ( B. stearothermophilus ) Minimal Φ-value analysis 1PHP [114] Phosphoglycerate kinase (Yeast) WT kinetics 3PGK [115] 

 α/β (RNase-H-like Motif) RNase-H-like RNase-H ( E.coli ) Hydrogen exchange Limited mutagenesis 1F21 [168,169] RNase-H ( T. thermophilus ) Hydrogen exchange 1RIL [170] [170,171] RNase-H ( C. tepidum ) WT kinetics 3H08 [171] 

 α/β (TIM β/α-barrel) Ribulose-phosphate binding barrel Trptophan synthase α-subunit [αTS] ( E. coli ) WT kinetics 1V7Y [116] [117] Indole-3-glycerophosphate synthase [sIGPS] ( S. solfataricus ) WT kinetics, Hydrogen exchange 1IGS [118,119] 

 Xylose isomerase-like IOLI ( B. subtilis ) WT kinetics 1I60 [117] 

 α + β (Ferredoxin-like) Acyl-phosphatase-like AcP (Human) Φ-Value analysis 1APS b [26,120] [26,65,121] HypF ( E. coli ) WT kinetics 1GXU [121] Protease propeptides/inhibitors Procarboxy-peptidase A2 (Human) Φ-Value analysis 1O6X [27] Ribosomal protein S6 S6 ( A. aeolicus ) Φ-Value analysis 2J5A [65] S6 ( T. thermophilus ) Φ-Value analysis 1RIS [69] RNA binding domain (RBD) U1A (Human) Φ-Value analysis 1FHT [13] 

 α + β (β-hairpin-α-hairpin repeat) Ankyrin repeat AnkyrinR D34 (Human) Minimal Φ-value analysis 1N11 [122] [123] Ankyrin repeats in tumor suppressor p16 (Human) Φ-Value analysis 1BI7 [52] Cell-cycle inhibitor p19ink4D (Human) WT kinetics 1BD8 [124] Myotrophin (Rat) Φ-Value analysis 2MYO [51] Neurogenic locus notch receptor domain (Drosophila) Minimal Φ-value analysis, WT redesign 1OT8 [125,126] 

 α + β (Cell-cycle regulatory proteins) Cell-cycle regulatory proteins CksHs1 (Human) Φ-Value analysis 1BUH [70] [70] CksHs2 (Human) WT kinetics 1CKS [127] Suc1 ( S. pombe ) Φ-Value analysis 1PUC [128] 

 α + β (Lysozyme-like) Lysozyme-like Lysozyme (Hen Egg White) WT kinetics 1E8L [129] [130] α-Lactalbumin (Bovine) WT kinetics 1F6S [130] α-Lactalbumin (Goat) Minimal Φ-value analysis, Hydrogen exchange 1HFY [131,132] [131] Milk lysozyme (Dog) Hydrogen exchange 1EL1 [131,133] 

 α + β (β-grasp: ubiquitin-like) Immunoglobulin-binding domains Protein G ( Streptococcus ) Φ-Value analysis 2IGD [42] [42,134,135] Immunoglobulin light chain-binding domain of Protein L ( P. magnus ) Φ-Value analysis 2PTL [41] Ubiquitin-like c-Raf1 RBD (Human) Φ-Value analysis 1RFA [134,135] Ubiquitin (Human) Minimal Φ-value analysis 1UBQ [136] Ubiquitin (Yeast) Φ-Value analysis 1Q0W [137] 

 All-β (Ig-like β-sandwich) Fibronectin type III CAfn2 ( B. circulans ) Φ-Value analysis 1K85 [19] [15,19] FnIII-9 (Human) WT kinetics 1FNF [138] FnIII-10 (Human) Φ-Value analysis 1FNF [16] TNfn3 (Human) Φ-Value analysis 1TEN [18] Immunoglobulin TI I27 (Human) Φ-Value analysis 1TIT [17] CD2 (Rat) Minimal Φ-value analysis 1HNG [37] Various antibody domains (V L , C L , C H 2, C H 3) WT kinetics [139–142] [142] 

 All-β (Lipocalins) Lipocalins CRABP I (Mouse) WT kinetics 2CBR [143,144] [32,143] CRBP II (Rat) WT kinetics 1OPA [143] IFABP (Rat) Minimal Φ-value analysis 1IFC [31,32,143,145] ILBP (Rat) Minimal Φ-value analysis 1O1V b [31,32] 

 All-β (OB-fold) Nucleic acid-binding proteins Bc-Csp ( B. caldolyticus ) Φ-Value analysis 1C9O [146,147] [146,148] CspA ( E. coli ) Hydrogen exchange 1MJC [149] Bs-CspB ( B. subtilis ) Φ-Value analysis 1CSP [150] Tm-Csp ( T. maritima ) WT kinetics 1G6P [148] 

 All-β (PDZ domain-like) PDZ domain-like PDZ2 domain from PTP-BL (Mouse) Φ-Value analysis 1GM1 [57] [151] Third PDZ domain from synaptic protein PSD-95 (Rat) Hydrogen exchange Φ-value analysis 1BE9 [151,152] 

 All-β (SH3-like barrel) Chromo domain-like DNA-binding protein Sso7d ( S. solfataricus ) Φ-Value analysis 1SSO [153] [21,153] SH3-domain α-Spectrin SH3-domain (Chicken) Φ-Value analysis, WT redesign 1SHG [22,154] Fyn proto-oncogene tyrosine kinase SH3-domain (Chicken) Φ-Value analysis, NMR dispersion 1FYN b [23,24,155,156] Actin binding protein ABP1 (Yeast) NMR dispersion 1JO8 [21] Phosphatidylinositol 3-kinase SH3-domain (Cow) WT kinetics 2PNI [157] c-src protein tyrosine kinase (Chicken) Φ-Value analysis 1SRM [25] 

 All-β (WW domain-like) WW domain Formin Binding Protein 28 (Mouse) Φ-Value analysis 1E0L [8,158]   Mitotic rotamase PIN1 (Human) Φ-Value analysis 1PIN [48,159] Yap65 WW domain (Human) WT kinetics 1JMQ [160] 

 Coiled coil proteins (Parallel coiled-coil) Leucine zipper domain GCN4 (Yeast) WT kinetics, Minimal Φ-value analysis 2BNI [161,162] c-Jun (Human) Dimer thermodynamics 1JUN [163] c-Fos (Human) Dimer thermodynamics 1FOS [163] a Comparative references are those in which the folding mechanisms/pathways of homologous proteins are compared and discussed.

Publication Year: 2010

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks.

(2010) BMC Bioinformatics 11 Suppl 1

PubMed: 20122223 | PubMedCentral: PMC3009521 | DOI: 10.1186/1471-2105-11-S1-S49

The hubs in PEN -15 (yellow VdW representation) in thermophilic PG Kinase, 1php (red cartoon representation), is considerably higher than in the corresponding mesophile, 3pgk (blue cartoon representat... on).

Table 1 Dataset taken for analysis Adenylate Kinases 1zip / 1ak2 Subtilisin 1thm / 1st3 Carboxypeptidases 1obr / 2ctc Neutal Proteases 1thl / 1npc Phosphofructo Kinases 3pfk / 2pfk Lactate Dehydrogenases 1ldn / 1ldm Glyceraldhyde-3-Phosphate Dehydrogenases 1vc2 / 1gad 3-Phosphoglycerate Kinases 1php / 3pgk Lipomide Dehydrogenases 1ebd / 1lvl Endo-1,4-Beta Xylanases 1yna / 1xyn Triose Phosphate Isomerases 1btm / 7tim Signal Recognition Particle Receptor 1ffh / 1fts The order of thermophile (bold)/mesophile pairs is the same as the order followed in generating all the Additional Figures (Fig S1 to S6).

Publication Year: 2010