Citations in PubMed

Primary Citation PubMed: 10512835 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 10

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.

(2007) Nucleic Acids Res 35

PubMed: 17913750 | PubMedCentral: PMC2190718 | DOI: 10.1093/nar/gkm711

NMR-based ( a ) folding topology and ( b ) solution structure of the bimolecular G-quadruplex formed by the d(GCGGT 3 GCGG) sequence in Na + solution (coordinates deposition: 1A6M) ( 164 ).

Publication Year: 2007


Automated main-chain model building by template matching and iterative fragment extension.

(2003) Acta Crystallogr D Biol Crystallogr 59

PubMed: 12499537 | PubMedCentral: PMC2745878 | DOI: null

This template consists of the average electron density calculated from a collection of α-helical segments six amino acids in length (from phycoerythrin; PDB code 1lia ; Chang et al. , 1996 &#x... 25b6; ; Berman et al. , 2000 ▶ ), all superimposed on a standard α-helical segment (from myoglobin; PDB code 1a6m ; Vojtechovsky et al. , 1999 ▶ ; Berman et al. , 2000 ▶ ).

Publication Year: 2003


Maximum-likelihood density modification using pattern recognition of structural motifs.

(2001) Acta Crystallogr D Biol Crystallogr 57

PubMed: 11717487 | PubMedCentral: PMC2745886 | DOI: null

Residues 133–138 of myoglobin (PDB entry 1a6m ) were chosen as a model helical segment.

Publication Year: 2001


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


Prediction of protein structural classes for low-homology sequences based on predicted secondary structure.

(2010) BMC Bioinformatics 11 Suppl 1

PubMed: 20122246 | PubMedCentral: PMC3009544 | DOI: 10.1186/1471-2105-11-S1-S9

The PDB IDs for four proteins are 1A6M (belonging to the α class), 1AJW (belonging to the β class), 1GQOV (belonging to the α / β class), and 1DEF (belonging to the &#x... 03b1; + β class).

Publication Year: 2010


Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns.

(2011) BMC Genomics 12 Suppl 4

PubMed: 22369665 | PubMedCentral: PMC3287581 | DOI: 10.1186/1471-2164-12-S4-S12

Three proteins with very different shapes were selected (a globin, PDB:1A6M; a porin, PDB:2ZFG; and a collagen, PDB:1BKV), and the topology of the contact graph obtained with different cutoffs is show... (6.0 Å, 9.0 Å and 12.0 Å).

Publication Year: 2011


Prediction of heme binding residues from protein sequences with integrative sequence profiles.

(2012) Proteome Sci 10 Suppl 1

PubMed: 22759579 | PubMedCentral: PMC3380730 | DOI: 10.1186/1477-5956-10-S1-S20

Given a heme binding protein sequence (PDB id: 1A6M; Chain: A), a window size of 3 is set for a simple illustration.

Publication Year: 2012


Towards accurate modeling of noncovalent interactions for protein rigidity analysis.

(2013) BMC Bioinformatics 14 Suppl 18

PubMed: 24564209 | PubMedCentral: PMC3817810 | DOI: 10.1186/1471-2105-14-S18-S3

A more quantitative approach was taken to validate dilution, confirming that the folding core identified by dilution agreed with the experimentally determined folding cores of 10 proteins: BPTI, 1bpi;... ubiquitin, 1ubi; CI2, 2ci2; ribonuclease T1, 1bu4; cytochrome c , 1hrc; barnase, 1a2p; α -lactalbumin, 1hml; apo-myoglogin, 1a6m; interleukin- β , 1ilb; T4 lysozyme, 3lzm [ 7 ].

Publication Year: 2013


Unfolding simulations of holomyoglobin from four mammals: identification of intermediates and ?-sheet formation from partially unfolded states.

(2013) PLoS One 8

PubMed: 24386077 | PubMedCentral: PMC3873898 | DOI: 10.1371/journal.pone.0080308

Calculated SASA and radius of gyration ( R g ) from crystal structures were based on averages of the structures 1A6M [87] , 1MBO [88] , 1U7S [66] , and 1U7R [66] for HoloMb.

State Conditions [θ] 222 (deg cm 2 dM −1 ) f H (%) SASA (nm 2 ) R g (nm) HoloN pH 7 −23,000 [9] ; −25,000 [10] 78 a 80.26 a 1.52 a (X-RAY); 1.8±0.2 [32] , [33] (SAXS) ApoN pH 7 −19,000±1000 [21] 53 [86] — 1.9±0.2 [34] (SAXS) ApoI pH 4, 0M Urea −12,000±1000 [21] <0.41 b — 2.3±0.2 [34] (SAXS) ApoU pH 5, 4.5M Urea −3000±1000 [21] ∼0 — 3.4±0.2 [34] (SAXS) a For HoloMb, average based on crystal structures 1A6M [84] , 1MBO [85] , 1U7S [65] , and 1U7R [65] .

Correspondingly, the radius of gyration ( R g ) was ∼1.51 nm for sperm whale and seal Mb and ∼1.48 and 1.50 nm for pig and horse Mb, averaged from 30–35 ns, in good agreement with the value of 1.52 nm from the average of R g for crystal structures of sperm whale and seal Mbs (PDB IDs: 1A6M [87] , 1MBO [88] , 1U7S [66] , 1U7R [66] , and 1MBS [90] ).

Publication Year: 2013


Macromolecular ab initio phasing enforcing secondary and tertiary structure.

(2015) IUCrJ 2

PubMed: 25610631 | PubMedCentral: PMC4285884 | DOI: 10.1107/S2052252514024117

The PDB ID codes for this set of tests are: 1a6m , 1byi , 1byz , 1c75 , 1eb6 , 1ejg , 1ew4 , 1fk5 , 1g2r , 1g2y , 1g4i , 1g6u , 1gvd , 1gxu , 1i2t , 1j8b , 1kth , 1l9l , 1n9b , 1oks , 1ox3 , 1pz4 , 1q... d , 1r7j , 1riy , 1rw1 , 1t07 , 1tgr , 1u84 , 1u9p , 1uj8 , 1use , 1usm , 1v2z , 1vyi , 1whz , 1wpa , 1y6x , 1yu5 , 1z96 , 1zva , 1zzk , 2b8i , 2c60 , 2ewt , 2f60 , 2fi0 , 2fq3 , 2fu2 , 2fvy , 2g7o , 2ggc , 2gkr , 2gpi , 2h8e , 2h9u , 2hdz , 2hl7 , 2hpj , 2i5f , 2igp , 2ip6 , 2ivy , 2nuh , 2o1k , 2o37 , 2o4t , 2o7a , 2oqq , 2ouf , 2oxo , 2p5k , 2p6v , 2pk8 , 2pst , 2q2f , 2qff , 2qmt , 2qsb , 2qvo , 2r31 , 2rhf , 2v75 , 2vkl , 2wuj , 2zqe , 2zqm , 2zxy , 3a4c , 3bri , 3ce7 , 3cec , 3cq1 , 3df8 , 3e21 , 3e9v , 3efg , 3fbl , 3fmy , 3g21 , 3g2b , 3g46 , 3goe , 3h01 , 3hro , 3idw , 3jsc , 3jtz , 3jvl , 3kp8 , 3mxz , 3o55 , 3oou , 3osh , 3qm9 , 3rq9 , 3s6e , 3soj , 3ui4 , 3vrc , 3wh1 , 3zzp , 4eic , 4g78 , 4g9s , 4hs1 , 4mzc , 4oo4 .

Publication Year: 2015