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PDB ID Mentions in PubMed Central Article count: 8

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Alignment of protein structures in the presence of domain motions.

(2008) BMC Bioinformatics 9

PubMed: 18727838 | PubMedCentral: PMC2535786 | DOI: 10.1186/1471-2105-9-352

For the alignment between the structures of the protein kinase domains of CDK6 ( 1BI7 ), MAPK P38 ( 1P38 ), Src ( 1FMK ), IGF1 receptor ( 1JQH ), EGFR ( 1M17 ), HGFR ( 1R0P ) and JAK3 ( 1YVJ ), the al... orithm implemented in DALI can cope with many cases of different relative domain orientation.

Publication Year: 2008


Simulation of different truncated p16(INK4a) forms and in silico study of interaction with Cdk4.

(2009) Cancer Inform 7

PubMed: 19352455 | PubMedCentral: PMC2664699 | DOI: null

Figure 5 a ) Complex structure of p16-Cdk6 available at Protein Data Bank (entry 1BI7).

Publication Year: 2009


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


The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors.

(2011) Mol Cancer 10

PubMed: 21575214 | PubMedCentral: PMC3123651 | DOI: 10.1186/1476-4598-10-54

Table 1 Overview of genes Gene name Length (AA) Mut SNP PDB codes (sequence range) Oncogenes AKT1 478 6 5 1UNQ A (1-123), 3CQW A (144-480) BRAF 766 46 3 3D4Q A (433-726), 3NY5 A (153-237) EGFR 1210 22... 9 1YY9 A (25-642), 1XKK A (695-1022) GNAS 394 12 9 1AZS C (1-394) HRAS 189 19 0 4Q21 A (1-189) KIT 976 9 9 2EC8 A (1-519), 3G0E A (544-935) KRAS 188 85 1 3GFT A (1-164) MET 1408 24 30 2UZX B (25-740), 3DKC A (1049-1360) NRAS 189 9 1 3CON A (1-172) PIK3CA 1068 148 17 2RD0 A (1-1068) PTPN11 593 7 6 2SHP A (3-529) RET 1114 24 3 2IVS A (705-1013), 2X2U A (29-270) Tumor Suppressor Genes CDH1 882 17 3 2O72 A (155-367) CDKN2A 156 76 10 1BI7 B (1-156) FBXW7 707 34 4 2OVR B (263-707) MLH1 756 8 3 3NA3 A (1-347) MSH2 934 12 17 2O8B A (1-934) PTEN 403 93 2 1D5R A (8-353) RB1 928 7 9 2R7G A (380-787), 2QDJ A (52-355), 2AZE C (829-874) SMAD4 552 51 3 1DD1 A (285-552) STK11 433 30 1 2WTK C (43-347) TP53 393 826 17 2VUK A (94-312), 1AIE A (326-356) VHL 213 216 16 1LM8 V (54-213) WT1 449 9 3 2PRT A (318-438) Abbreviations: AA, amino acid, Mut, number of mutations, SNP, number of SNPs, PDB, Protein Data Bank Single nucleotide polymorphism dataset ( Snp ) As a control set, we extracted single nucleotide polymorphism (SNP) data for the 24 genes from version 131 of the common variation database dbSNP [ 17 ].

Publication Year: 2011


Selective anticancer activity of a hexapeptide with sequence homology to a non-kinase domain of Cyclin Dependent Kinase 4.

(2011) Mol Cancer 10

PubMed: 21668989 | PubMedCentral: PMC3126777 | DOI: 10.1186/1476-4598-10-72

Table 1 Quality and accuracy scores for the built models MODEL Model 1 Model 2 Model 3 Model 4 Model 5 Template 1BLX (CDK6) 1G3N (CDK6) Base template 1BLX , Variable regions differing by more than 2.0... Å rmsd modelled from 1G3N , 1BI8 , 1BI7 and 1JOW (all CDK6) Base template 1BLX , Variable regions differing by more than 2.0 Å rmsd.

Publication Year: 2011


Comparative modeling and docking studies of p16ink4/cyclin D1/Rb pathway genes in lung cancer revealed functionally interactive residue of RB1 and its functional partner E2F1.

(2013) Theor Biol Med Model 10

PubMed: 23276293 | PubMedCentral: PMC3563505 | DOI: 10.1186/1742-4682-10-1

Table 1 Templates sorted by their overall quality Z-scores and E-values Protein Model ID Z-Score Alignment BLAST E-value RB1 4ELJ-A −0.007 Good 0 P16-INK4A 1MX6-B −0.289 Optimal 7e-032...   1BLX-B −0.528 Good 1e-034   1BD8-A −0.620 Good 2e-036   1BI7-B −1.084 Good 6e-042   2A5E-A −2.110 Good 9e-050 Hybrid structure of RB1 protein was generated using best aligned parts of templates (Figure 1 ).

Publication Year: 2013


Assessment of computational methods for predicting the effects of missense mutations in human cancers.

(2013) BMC Genomics 14 Suppl 3

PubMed: 23819521 | PubMedCentral: PMC3665581 | DOI: 10.1186/1471-2164-14-S3-S7

the protein structure (PDB id: 1BI7) illustrates CDKN2A (wheat color) in complex with CDK6 (blue).

Publication Year: 2013


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4373711

Repeat protein TPR pdb code Natural resolution (Å) No of repeats Template pdb code Template resolution (Å) Identity (%) RMSD TPR 3EJN: A 1.50 Tpr like 4LER: A 1.42 54.1 1.133 2C0M: A 2... 50 8 4EQF: A 3.00 62.3 2.447 3CEQ: B 2.75 5.5 3NF1: A 2.80 81.0 2.578 3FP3: A 1.98 11 2GW1: A 3.00 58.5 2.414 3SF4: A 2.60 8 4A1S: A 2.10 64.7 1.519 3U84: A 2.50 3 3RE2: A 1.95 54.2 1.098 4AM9: A 2.50 3 2XCB: A 1.85 61.8 1.027 4GCO: A 1.60 3 2LNI: A NMR 58.3 2.114 Ankyrin 1AWC: B 2.15 5 2P2C: P 3.24 69.9 1.193 1BI7: B 3.40 4 1D9S: A NMR 86.4 1.690 1YCS: B 2.20 3 2VGE: A 2.10 59.2 1.071 2ETB: A 1.65 6 2F37: A 1.70 86.2 1.020 1YYH: A 1.90 6 1OT8: A 2.00 74.6 0.670 3V30: A 1.57 5 3SO8: A 1.90 65.8 1.099 1MJ0: A 2.03 5 2BKK: B 2.15 84.6 1.263 1OT8: A 2.00 6 2F8Y: A 1.55 73.2 1.289 Results and Discussion Statistical potentials based on general and α+β proteins Recently, we evaluated the stability of self-derived peptides derived from three classes of envelope (E) proteins by two state-of-art statistical scoring functions, dDFIRE and RAPDF[ 17 ], [ 34 ].

Publication Year: 2015