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PDB ID Mentions in PubMed Central

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Global analysis of posttranslational protein arginylation.

(2007) PLoS Biol 5

PubMed: 17896865 | PubMedCentral: PMC1988855 | DOI: 10.1371/journal.pbio.0050258

Figure 6 Structural Models of Proteins Regulated by Arginylation Three-dimensional structures of proteins downloaded from the National Center for Biotechnology Information structure database at http:/... www.ncbi.nlm.nih.gov/ (PDB identifiers 1HLU for beta actin, 1TUB for tubulin, 1DXT for hemoglobin, and 1ZNQ for GADPH) with arginylated positions highlighted in yellow within the polypeptide chains and marked with red letters R. Alpha and beta for tubulin indicate the corresponding polypeptide chains.

To further assess the possible role of arginylation in modulating the activity of the proteins found on our list, we selected a few targets from our list whose biological role is well characterized and for which three-dimensional structures are available in a public database, including non-muscle actin (PDB identifier 1HLU), tubulin (1TUB), hemoglobin (1DXT), GAPDH (1ZNQ), ARP3 (as part of ARP2/3 complex, 1K8K), 8-kDa dynein light chain (1PWK), and fragment of calmodulin in complex with spectrin (2FOT).

Publication Year: 2007


Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations.

(2009) BMC Struct Biol 9

PubMed: 19917096 | PubMedCentral: PMC2783033 | DOI: 10.1186/1472-6807-9-71

Comparison of RMSD of the C α trace of a decoy conformer (model 113) of target 1dxt in MOULDER and its residue-position Zscores Sc , ScZE min , and Z A E min .

Table 6 Correlation between RMSD and residue-position Zscores Target Set C(ΔZ A E min ) C L (Z A E min ) C(ΔScZE min ) C L (ScZE min ) Average P/N Average P/N Average P/N Average P/N Average P/N Average P/N Average P/N Average P/N 1bbh 0.7 ± 0.1 124/34 0.7 ± 0.1 82/76 0.7 ± 0.1 135/23 0.7 ± 0.1 109/49 0.7 ± 0.1 112/46 0.6 ± 0.1 37/121 0.6 ± 0.1 92/66 0.7 ± 0.1 56/102 1c2r 0.7 ± 0.1 87/22 0.6 ± 0.2 25/84 0.7 ± 0.1 62/47 0.6 ± 0.2 23/36 0.5 ± 0.2 10/99 0.6 ± 0.2 13/96 0.5 ± 0.2 6/103 0.5 ± 0.2 5/104 1cau 0.6 ± 0.2 22/16 0.7 ± 0.2 28/10 0.5 ± 0.2 4/34 0.7 ± 0.2 28/10 0.6 ± 0.2 11/27 0.7 ± 0.2 26/12 0.5 ± 0.2 7/31 0.6 ± 0.2 19/19 1cew 0.8 ± 0.0 1/11 0.5 ± 0.3 3/9 0.6 ± 0.0 1/11 0.8 ± 0.0 1/11 0.6 ± 0 1/11 0.5 ± 0.4 2/10 0.0 ± 0.0 0/12 0.8 ± 0.0 1/11 1cid 0.7 ± 0.1 56/27 0.8 ± 0.2 52/31 0.7 ± 0.1 60/23 0.7 ± 0.1 59/24 0.8 ± 0.1 77/6 0.7 ± 0.2 28/55 0.8 ± 0.1 80/3 0.7 ± 0.2 28/55 1dxt 0.6 ± 0.1 44/106 0.7 ± 0.1 89/61 0.6 ± 0.1 79/71 0.7 ± 0.1 111/39 0.5 ± 0.2 6/144 0.7 ± 0.2 46/104 0.5 ± 0.2 8/142 0.7 ± 0.1 56/94 1eaf 0.5 ± 0.2 10/50 0.6 ± 0.2 18/42 0.6 ± 0.2 15/45 0.5 ± 0.1 22/38 0.4 ± 0.2 3/57 0.6 ± 0.2 17/43 0.4 ± 0.2 3/57 0.6 ± 0.1 28/32 1gky 0.6 ± 0.2 12/17 0.7 ± 0.2 14/5 0.5 ± 0.2 5/14 0.6 ± 0.2 14/5 0.6 ± 0.2 13/6 0.6 ± 0.2 10/9 0.6 ± 0.2 13/6 0.7 ± 0.2 12/7 1lga 0.5 ± 0.2 12/95 0.5 ± 0.2 10/97 0.5 ± 0.2 9/98 0.5 ± 0.2 5/102 0.6 ± 0.0 1/106 0.5 ± 0.2 8/99 0.4 ± 0.3 2/105 0.4 ± 0.3 3/104 1mdc 0.7 ± 0.1 59/56 0.7 ± 0.2 42/73 0.7 ± 0.1 68/47 0.7 ± 0.2 47/68 0.6 ± 0.1 39/76 0.6 ± 0.1 28/87 0.6 ± 0.2 16/99 0.6 ± 0.2 18/97 1mup 0.7 ± 0.1 60/74 0.7 ± 0.1 73/61 0.7 ± 0.1 68/66 0.7 ± 0.1 77/57 0.7 ± 0.1 99/35 0.7 ± 0.1 59/75 0.7 ± 0.1 112/22 0.7 ± 0.1 53/81 1onc 0.7 ± 0.2 53/69 0.6 ± 0.2 29/93 0.7 ± 0.2 59/63 0.7 ± 0.2 38/84 0.7 ± 0.1 102/20 0.7 ± 0.2 43/79 0.7 ± 0.1 86/36 0.7 ± 0.1 40/82 2afn 0.6 ± 0.1 80/39 0.6 ± 0.1 73/46 0.6 ± 0.1 22/97 0.6 ± 0.1 71/48 0.5 ± 0.1 25/94 0.5 ± 0.2 18/103 0.5 ± 0.2 9/110 0.5 ± 0.1 17/102 2cmd 0.7 ± 0.1 101/128 0.6 ± 0.1 112/117 0.6 ± 0.1 93/136 0.6 ± 0.1 103/126 0.6 ± 0.1 102/127 0.6 ± 0.1 50/179 0.6 ± 0.1 42/187 0.6 ± 0.1 58/171 2fbj 0.6 ± 0.2 12/89 0.6 ± 0.1 24/77 0.6 ± 0.2 7/94 0.6 ± 0.2 13/88 0.6 ± 0.1 32/69 0.6 ± 0.2 11/90 0.6 ± 0.1 40/61 0.6 ± 0.1 19/82 2mta 0.6 ± 0.1 47/111 0.7 ± 0.1 48/110 0.7 ± 0.1 75/83 0.7 ± 0.2 32/126 0.7 ± 0.1 104/54 0.7 ± 0.1 73/85 0.7 ± 0.1 130/28 0.6 ± 0.2 40/118 2pna 0.7 ± 0.1 41/97 0.7 ± 0.1 73/65 0.7 ± 0.2 37/101 0.7 ± 0.1 71/67 0.0 ± 0.0 0/138 0.7 ± 0.2 67/71 0.6 ± 0.2 12/126 0.7 ± 0.2 59/79 2sim 0.5 ± 0.2 4/90 0.4 ± 0.3 3/91 0.0 ± 0.0 0/94 0.6 ± 0.0 1/93 0.4 ± 0.3 2/92 0.6 ± 0.0 1/93 0.4 ± 0.3 2/92 0.0 ± 0.0 0/94 4sbv 0.5 ± 0.4 2/2 0.4 ± 0.3 2/2 0.4 ± 0.3 2/2 0.4 ± 0.3 2/2 0.0 ± 0.0 0/4 0.0 ± 0.0 0/4 0.0 ± 0.0 0/4 0.0 ± 0.0 0/4 8i1b 0.4 ± 0.3 2/135 0.6 ± 0.2 11/126 0.5 ± 0.2 5/132 0.6 ± 0.2 13/124 0.6 ± 0.1 43/94 0.5 ± 0.1 18/119 0.5 ± 0.1 23/114 0.6 ± 0.2 13/124 Pearson correlation between RMSD of C α atoms and residue-position Zscores of structure-models in MOULDER decoy set.

Target ZE min ZE Aa3DEnv -min ZE 3DEnv -min ZE local -min 1bbh 0.86 0.36 -0.83 -0.80 0.62 0.42 -0.02 -0.71 1c2r 0.71 0.45 -0.48 -0.67 0.69 0.68 -0.43 -0.27 1cau 0.83 0.56 -0.71 -0.72 0.69 0.38 -0.40 -0.74 1cew 0.70 0.31 -0.64 -0.58 0.61 0.08 -0.18 -0.63 1cid 0.41 -0.12 -0.22 -0.59 0.45 0.43 0.10 -0.55 1dxt 0.87 0.75 -0.84 -0.76 0.78 0.76 -0.51 -0.51 1eaf 0.79 0.57 -0.61 -0.64 0.72 0.66 -0.38 -0.55 1gky 0.88 0.54 -0.77 -0.78 0.73 0.61 -0.18 -0.63 1lga 0.88 0.49 -0.68 -0.85 0.84 0.68 -0.40 -0.84 1mdc 0.78 0.50 -0.51 -0.64 0.68 0.40 -0.20 -0.60 1mup 0.85 0.66 -0.80 -0.83 0.80 0.79 0.24 -0.79 1onc 0.78 0.66 -0.58 -0.58 0.80 0.75 -0.29 -0.56 2afn 0.86 0.61 -0.60 -0.83 0.77 0.68 -0.27 -0.83 2cmd 0.81 0.68 -0.82 -0.78 0.63 0.58 -0.46 -0.65 2fbj 0.77 0.35 -0.32 -0.82 0.79 0.58 -0.13 -0.83 2mta 0.72 0.47 -0.16 -0.69 0.77 0.67 -0.02 -0.70 2pna 0.83 0.58 -0.79 -0.55 0.62 0.52 -0.29 -0.46 2sim 0.81 -0.12 -0.73 -0.81 0.66 0.20 -0.36 -0.76 4sbv 0.69 -0.10 -0.65 -0.60 0.54 0.46 -0.07 -0.45 8i1b 0.77 0.68 -0.36 -0.60 0.57 0.67 0.13 -0.43 Pearson product-correlation between Root Mean Square Deviation (RMSD) of MOULDER decoys of 20 target/model sets (in rows) and Zscores (in columns): , , , , ZE min , ZE S3DC -min , ZE 3DC -min , and ZE local -min .

b) RMSD is compared with the difference of residue-position Zscores between the model and the native structure ( 1dxt ).

Target set DOPE GA341 Prosa2003 DFIRE ZEmin fisa_casp3 1eh2 6,06 4,64 1,64 4,93 4,13 4,93 1bg8 -A 7,84 7,28 7,28 3,58 5,72 3,58 1jwe 6,30 10,62 9,75 8,10 9,52 8,10 1bl0 4,10 2,24 2,24 7,10 4,45 7,10 smd3 4,35 6,44 5,08 5,12 5,32 4,47 Average 5,73 6,25 5,20 5,76 5,83 5,63 lmds 1dtk 5,46 4,75 4,59 4,59 4,89 2,90 1igd 7,64 1,63 4,28 5,61 4,50 5,61 2cro 8,68 8,95 6,14 10,01 5,93 9,48 smd3 4,35 4,52 2,68 5,52 2,50 5,52 1ctf 9,41 7,65 7,52 7,37 6,67 7,37 1fc2 0,26 0,51 1,00 0,07 1,51 0,07 1shf -A 5,83 5,16 3,06 6,91 5,24 6,91 4pti 5,64 5,72 9,91 4,61 9,54 4,61 2ovo 6,92 3,49 6,45 5,70 7,26 5,70 1b0n -B 1,60 2,20 0,61 0,50 1,76 0,50 1bba 1,89 0,87 0,59 3,29 2,00 1,92 Average 5,24 4,13 4,26 4,92 4,71 4,60 4state_reduced 1sn3 1,69 0,90 4,09 4,71 6,05 0,90 1r69 2,55 0,80 0,79 0,95 2,29 0,79 4pti 0,82 5,53 0,07 0,07 1,18 2,80 2cro 2,46 1,24 0,29 1,24 0,53 0,53 1ctf 0,33 0,60 0,50 2,93 1,02 1,02 3icb 1,86 1,51 0,93 0,11 0,05 0,11 4rxn 0,46 3,52 0,75 0,70 0,68 0,70 Average 1,45 2,01 1,06 1,53 1,69 0,98 MOULDER 1onc 1,16 0,72 0,60 0,40 0,40 0,40 1dxt 3,97 0,00 0,55 1,11 0,00 0,55 1eaf 0,34 1,72 1,72 0,47 0,99 0,47 1lga 0,82 5,89 5,89 0,80 0,00 0,80 1gky 0,57 0,34 0,57 0,57 0,62 0,57 1cau 3,89 1,95 0,42 0,42 0,07 0,42 4sbv 0,00 5,57 0,00 0,00 6,43 0,00 8i1b 0,38 0,42 0,39 0,50 0,36 1,04 2mta 0,31 0,57 0,21 0,63 0,32 0,63 2cmd 0,38 2,22 0,58 0,23 0,74 0,84 2fbj 0,26 2,80 0,32 0,91 0,51 0,91 1cew 2,06 2,73 2,73 3,47 3,73 3,47 2afn 0,71 0,75 0,68 0,12 0,50 0,12 2sim 1,21 0,42 0,46 0,16 1,13 0,16 1bbh 0,88 0,11 0,16 0,00 0,31 0,00 1mdc 0,03 0,74 6,85 0,16 0,00 0,16 1mup 0,53 0,17 0,67 0,67 0,32 0,46 2pna 0,26 0,60 0,42 0,24 0,26 0,24 1cid 1,15 1,15 1,15 0,08 1,15 1,15 1c2r 3,42 0,00 0,85 0,00 0,00 0,15 Average 1,12 1,44 1,26 0,55 0,89 0,63 In the first column it is shown the code of the target protein used to generate the set of decoys.

d) The native structure of 1dxt is shown in ribbons (green) superposed with the structure of the near-native decoy (model 113, in cyan), showing the fragments with higher residue-position Zscores and RMSD in orange (native) and yellow (model 113).

Target set DOPE GA341 Prosa2003 DFIRE ZEmin fisa_casp3 smd3 1 51 2 1 12 1 1bg8 -A 1 808 151 1 341 2 1jwe 1 135 4 1 514 1 1eh2 8 826 93 1 577 159 1bl0 1 809 729 1 458 3 Total 4 0 0 5 0 2 lmds smd3 1 15 1 1 1 1 2ovo 7 33 1 61 115 7 1dtk 1 1 1 1 77 33 4pti 6 7 1 24 25 10 1b0n -B 293 35 1 418 99 180 1bba 501 395 458 501 389 63 1shf -A 1 5 13 1 199 1 1ctf 1 1 1 1 1 1 1fc2 501 234 107 501 276 489 1igd 1 1 1 18 10 1 2cro 1 10 1 1 43 16 Total 6 3 8 5 2 4 4state_reduced 4rxn 1 1 8 1 20 26 4pti 1 6 1 1 1 1 1ctf 1 1 1 1 1 1 3icb 3 5 1 5 10 9 1sn3 1 1 1 1 25 3 2cro 1 5 1 1 1 2 1r69 1 4 1 1 1 1 Total 6 3 6 6 4 3 MOULDER 1onc 1 1 1 1 1 1 1dxt 1 1 1 1 3 1 1eaf 1 1 1 1 1 1 1lga 1 1 1 1 1 1 1gky 1 1 1 1 1 1 1cau 1 1 1 1 1 1 4sbv 1 1 1 1 1 1 8i1b 1 1 1 1 1 1 2mta 1 1 1 1 4 4 2fbj 1 1 1 1 1 1 2cmd 1 1 1 1 1 1 1cew 1 1 1 1 1 1 2afn 1 1 1 1 1 1 2sim 1 1 1 1 1 1 1bbh 1 1 1 1 1 1 1mdc 1 1 1 1 1 1 1mup 1 1 1 1 15 1 2pna 85 45 43 85 58 9 1cid 1 1 1 1 1 1 1c2r 1 1 1 1 6 1 Total 19 19 19 19 15 18 Ranking position of the native structure among the sets of model/target decoys for several scoring functions.

Figure 3 Ribbon plot of 1dxt native and decoy structures .

Figure 3 shows the superposition of the native structure with the best and the worst candidates from the decoys of target " 1dxt " in MOULDER.

Ribbon plot of the native structure (in green) superposed with the model decoys (in cyan) of the target 1dxt in MOULDER.

Figure 8 Comparison of RMSD and residue-position Zscores for target 1dxt in MOULDER .

Publication Year: 2009


In silico analysis of single nucleotide polymorphism (SNPs) in human ?-globin gene.

(2011) PLoS One 6

PubMed: 22028795 | PubMedCentral: PMC3197589 | DOI: 10.1371/journal.pone.0025876

Previously, the HBB gene (PDB ID: 1DXT) have been analyzed for native and mutant protein structures [35] .

Publication Year: 2011