Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 19

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Tools for integrated sequence-structure analysis with UCSF Chimera.

(2006) BMC Bioinformatics 7

PubMed: 16836757 | PubMedCentral: PMC1570152 | DOI: 10.1186/1471-2105-7-339

Table 2 Results from different programs for difficult structure pairs pair PDB ID PDB ID Chimera TOPOFIT CE CE/MA 1 3chy 2fox 88/2.2 19/0.7 108/3.6 93/2.6 2 2aza A 1paz 79/2.0 72/1.7 84/2.9 81/2.4 3 1... ew I 1mol A 73/1.9 73/1.6 81/2.3 78/1.9 4 1cid 2rhe 90/2.0 69/1.5 97/2.9 88/1.9 5 1crl 1ede 184/2.5 143/1.9 219/3.8 183/2.3 6 2sim 1nsb A 257/2.6 207/2.0 275/3.0 266/2.5 7 1ten 3hhr B 82/1.3 81/1.4 87/1.9 85/1.6 8 1tie 4fgf 73/2.2 88/1.6 116/2.9 105/2.1 9 2snv 5ptp 118/2.3 83/1.8 130/3.1 118/2.4 10 1gp1 A 2trx A 89/1.8 96/1.6 64/5.2 54/2.7 Results are of the form N/RMSD, where N is the number of residue pairs matched and RMSD is the corresponding alpha-carbon root-mean-square deviation.

Publication Year: 2006


Functional site prediction selects correct protein models.

(2008) BMC Bioinformatics 9 Suppl 1

PubMed: 18315844 | PubMedCentral: PMC2259414 | DOI: 10.1186/1471-2105-9-S1-S13

Training-set proteins: 3chy (Chemotaxis Y protein), 1coz (Glycerol-3-phosphate cytidylyltransferase), 1di0 (Lumazine synthase), 2trx (Thioredoxin), 1f4p (Flavodoxin).

For 2trx , F1 (thick green line) corresponds to the correct fold.

Figures 3a and 3b shows the "proximity plots" of the best models in each fold-type for Chemotaxis Y protein ( 3chy ) and Thioredoxin ( 2trx ).

Figure 3 Example "proximity plots" for 3chy and 2trx .

The Specificity-Sensitivity curves for each of the five training-set proteins (a) 3chy , (b) 1coz , (c) 2trx , (d) 1f4p and (e) 1di0 using "Fold Score" (red) are shown.

The "proximity plots" for the best models of each fold-type for (a) Chemotaxis Y protein ( 3chy ) and (b) Thioredoxin protein ( 2trx ) are shown.

By contrast, CRESCENDO predicted one binding site for the Thioredoxin protein ( 2trx ) and 100% of the top 5 pairs of residues are within 12 Å distance (Figure 3b ).

The thick blue line indicates the native crystal structure in both 3chy and 2trx plots.

The "summary plots" for each of the five training-set proteins (a) 3chy , (b) 1coz , (c) 2trx , (d) 1f4p and (e) 1di0 are shown.

Publication Year: 2008


Properties of the thioredoxin fold superfamily are modulated by a single amino acid residue.

(2009) J Biol Chem 284

PubMed: 19181668 | PubMedCentral: PMC2665069 | DOI: 10.1074/jbc.M809509200

B, ribbon diagrams of the structures of E. coli DsbA (PDB code 1FVK ( 54 )), the thioredoxin domain of DsbC (oriented using DsbA as a reference; PDB code 1EEJ ( 39 )), thioredoxin (PDB code 2TRX ( 55 ... ), and thioredoxin I75T variant (PDB code 3DYR (this work)).

The structure was solved by molecular replacement as implemented in the CNS program ( 32 ) using the WT E. coli thioredoxin structure as a search model (2TRX).

Publication Year: 2009


RBT-GA: a novel metaheuristic for solving the Multiple Sequence Alignment problem.

(2009) BMC Genomics 10 Suppl 1

PubMed: 19594869 | PubMedCentral: PMC2709253 | DOI: 10.1186/1471-2164-10-S1-S10

In several other cases, RBT-GA's performance was just fairly comparable to the others, like 1uky , 1tgxA and 2trx .

Publication Year: 2009


Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy.

(2009) Nat Struct Mol Biol 16

PubMed: 19597482 | PubMedCentral: PMC2745927 | DOI: 10.1038/nsmb.1627

(B) Groove depth for three eukaryotic-origin Trxs (red): human Trx1 (pdb:1mdi); A. thaliana Trx h 1 (pdb:1xfl) and spinach Trx f (pdb:1f9m), and three bacterial-origin Trxs (blue): human Trx2 (pdb:1uv... ); E. coli Trx1 (pdb:2trx) and C. reinhardtii Trx m (pdb:1dby).

Publication Year: 2009


Structural alphabets derived from attractors in conformational space.

(2010) BMC Bioinformatics 11

PubMed: 20170534 | PubMedCentral: PMC2838871 | DOI: 10.1186/1471-2105-11-97

PDB ID Chain SCOP superfamily classification H+E/L size 1a4p A a.39.1 3.18 92 2dn2 C a.1.1 2.92 141 2ilk A a.26.1 2.16 155 1v74 B a.24.20 1.81 87 2hue C a.22.1 1.34 82 1mz4 A a.3.1 1.30 131 1z5y D b.1... 17 2.11 118 1n9r G b.38.1 2.09 68 2f3g B b.84.3 1.21 150 2z6k D b.40.4 1.09 117 2rac A b.6.1 0.91 105 1beh B b.17.1 0.69 183 1ay7 B c.9.1 2.30 89 1qjc B c.26.1 1.85 157 2vrw A c.37.1 1.49 177 2d1p B c.114.1 1.43 119 2trx B c.47.1 1.30 108 1uex C c.62.1 1.22 202 1gy6 B d.17.4 3.10 123 1oo0 A d.232.1 2.06 144 1gd0 C d.80.1 1.74 118 3eze B d.94.1 1.58 85 2uyz A d.20.1 1.20 156 2inc C d.15.12 1.07 83 H+E/L: ratio between regular (H+E) and irregular (L) secondary structure elements according to DSSP [ 55 ] (H+E = H+G+I+E and L = T+S+unassigned in the DSSP dictionary); size: number of residues.

M32K25 CGT2004 MSM2000 PDB ID Chain R(LF) R(GF) R(LF) R(GF) R(LF) R(GF) 1a4p A 0.772 0.700 0.258 0.178 0.852 0.493 2dn2 C 0.729 0.645 -0.062 0.169 0.638 0.133 2ilk A 0.851 0.770 0.428 0.501 0.909 0.658 1v74 B 0.866 0.805 0.390 0.419 0.862 0.618 2hue C 0.875 0.795 0.383 0.295 0.910 0.594 1mz4 A 0.672 0.515 0.195 0.228 0.734 0.452 1z5y D 0.617 0.477 0.659 0.502 0.712 0.395 1n9r G 0.554 0.358 0.569 0.440 0.473 0.373 2f3g B 0.557 0.325 0.444 0.287 0.439 0.295 2z6k D 0.772 0.591 0.601 0.580 0.816 0.597 2rac A 0.686 0.431 0.754 0.568 0.804 0.518 1beh B 0.652 0.490 0.550 0.369 0.726 0.630 1ay7 B 0.564 0.502 -0.137 -0.247 0.638 0.126 1qjc B 0.616 0.483 0.119 0.172 0.738 0.504 2vrw A 0.763 0.536 0.455 0.372 0.838 0.641 2d1p B 0.759 0.598 0.451 0.388 0.772 0.539 2trx B 0.716 0.435 0.494 0.299 0.780 0.560 1uex C 0.790 0.545 0.452 0.369 0.881 0.676 1gy6 B 0.654 0.534 0.344 0.308 0.649 0.371 1oo0 A 0.812 0.624 0.362 0.399 0.799 0.483 1gd0 C 0.724 0.600 0.435 0.468 0.753 0.516 3eze B 0.580 0.388 0.098 -0.194 0.470 0.373 2uyz A 0.744 0.574 0.243 0.331 0.829 0.447 2inc C 0.728 0.514 0.535 0.424 0.716 0.428 R(LF) and R(GF): Pearson correlation coefficients between fragment RMSF and Shannon Entropy of local fit (LF) and global fit (GF) encoding.

M32K25 LF M32K25 GF CGT2004 LF CGT2004 GF MSM2000 LF MSM2000 GF PDB ID /Å IQD/Å /Å IQD/Å /Å IQD/Å /Å IQD/Å /Å IQD/Å /Å IQD/Å 1a4p 0.225 0.014 0.664 0.037 0.207 0.014 0.575 0.046 0.261 0.012 1.005 0.034 2dn2 0.203 0.009 0.659 0.045 0.192 0.009 0.541 0.043 0.260 0.008 1.017 0.028 2ilk 0.261 0.013 0.771 0.046 0.237 0.013 0.673 0.053 0.286 0.011 1.024 0.025 1v74 0.218 0.016 0.653 0.046 0.209 0.015 0.559 0.049 0.280 0.014 1.018 0.025 2hue 0.250 0.017 0.700 0.045 0.230 0.016 0.622 0.051 0.291 0.014 1.001 0.029 1mz4 0.273 0.013 0.756 0.032 0.260 0.011 0.667 0.030 0.317 0.011 0.960 0.023 1z5y 0.308 0.021 0.852 0.085 0.307 0.016 0.873 0.082 0.356 0.015 0.940 0.055 1n9r 0.328 0.020 0.844 0.061 0.310 0.017 0.803 0.049 0.352 0.016 0.847 0.032 2f3g 0.294 0.011 0.808 0.026 0.299 0.011 0.798 0.025 0.338 0.009 0.854 0.017 2z6k 0.300 0.015 0.811 0.048 0.298 0.013 0.807 0.039 0.333 0.013 0.883 0.024 2rac 0.308 0.017 0.810 0.050 0.307 0.015 0.819 0.051 0.354 0.013 0.869 0.025 1beh 0.313 0.013 0.863 0.034 0.305 0.011 0.831 0.032 0.351 0.008 0.925 0.016 1ay7 0.248 0.014 0.654 0.030 0.239 0.015 0.601 0.045 0.307 0.013 0.963 0.025 1qjc 0.262 0.012 0.725 0.026 0.253 0.010 0.666 0.028 0.307 0.010 0.957 0.021 2vrw 0.268 0.013 0.721 0.028 0.264 0.013 0.688 0.031 0.311 0.012 0.912 0.015 2d1p 0.275 0.018 0.749 0.032 0.269 0.016 0.718 0.032 0.331 0.014 0.913 0.023 2trx 0.305 0.016 0.763 0.032 0.289 0.015 0.703 0.035 0.328 0.011 0.929 0.023 1uex 0.279 0.012 0.763 0.029 0.265 0.010 0.722 0.028 0.318 0.014 0.975 0.018 1gy6 0.271 0.023 0.807 0.094 0.259 0.019 0.788 0.096 0.328 0.020 0.955 0.059 1oo0 0.279 0.020 0.797 0.071 0.263 0.018 0.739 0.072 0.320 0.016 0.969 0.039 1gd0 0.286 0.017 0.819 0.046 0.266 0.015 0.757 0.053 0.337 0.014 0.959 0.038 3eze 0.284 0.017 0.735 0.036 0.269 0.016 0.694 0.047 0.314 0.015 0.921 0.042 2uyz 0.268 0.015 0.745 0.044 0.268 0.013 0.745 0.045 0.313 0.011 0.946 0.022 2inc 0.268 0.016 0.728 0.052 0.285 0.016 0.744 0.049 0.324 0.014 0.878 0.035 : median cRMSD, IQD: inter-quartile distance of cRMSD.

Publication Year: 2010


Role of conservative mutations in protein multi-property adaptation.

(2010) Biochem J 429

PubMed: 20446918 | PubMedCentral: PMC2895784 | DOI: 10.1042/BJ20100386

Briefly, BLAST2 ( http://blast.wust1.edu ) was used to search the sequence of E. coli thioredoxin with the PDB code 2TRX as the query in the UniProt database with default search options.

Publication Year: 2010


Thioredoxin A active-site mutants form mixed disulfide dimers that resemble enzyme-substrate reaction intermediates.

(2008) J Mol Biol 379

PubMed: 18455736 | PubMedCentral: PMC2896474 | DOI: 10.1016/j.jmb.2008.03.077

It is also similar to the known human and E. coli structures (PDB codes 2TRX , 1XOA , 1XOB , 1ERU , 1ERT , 1CQG , 1CQH , and 1MDJ ) with rmsd values of 1–1.5Å for global C α su... erpositions.

53 Molecular replacement was performed using the program PHASER 54 in the CCP4 program suite, with a polyserine model of TrxA from E. coli (PDB code 2TRX ) as the initial model.

Publication Year: 2008


A signal processing method to explore similarity in protein flexibility.

(2010) Adv Bioinformatics

PubMed: 21197478 | PubMedCentral: PMC3010618 | DOI: 10.1155/2010/454671

In this case, the parameters were determined form E. coli protein (PDB code 2TRX), and the same parameters were used to generate QSFR for orthologous thioredoxins from Anabaena species (1THX), Chlamyd... monas reinhardtii (1EP7), and Spinacia oleracea (1FB6).

Publication Year: 2010


Oxidation state-dependent protein-protein interactions in disulfide cascades.

(2011) J Biol Chem 286

PubMed: 21543317 | PubMedCentral: PMC3137068 | DOI: 10.1074/jbc.M111.236141

The structures shown are from the following PDB entries: nDsbD ( 1JPE ( 16 )), cDsbD ( 2FWF ( 21 )), Trx ( 2TRX ( 53 )), DsbC ( 1EEJ ( 54 )), CcmG ( 2B1K ( 55 )).

Publication Year: 2011


Protein design using continuous rotamers.

(2012) PLoS Comput Biol 8

PubMed: 22279426 | PubMedCentral: PMC3257257 | DOI: 10.1371/journal.pcbi.1002335

The structures for the training set (PDB ids: 1fus, 1ifc, 1lkk, 1plc, 1poa, 1rro, 1whi, 2rhe, and 2trx) were selected from the Richardson's Top 100 database of high-quality curated protein structures ... 43] .

Publication Year: 2012


The interplay between the disulfide bond formation pathway and cytochrome c maturation in Escherichia coli.

(2012) FEBS Lett 586

PubMed: 22569094 | PubMedCentral: PMC3420020 | DOI: 10.1016/j.febslet.2012.04.055

The PDB entries used are 2TRX , 1FVK , 2HI7 , 2FWH , 1JPE , 2BLK , 2E2E , and 155C .

Publication Year: 2012


Combinatorial library of improved peptide aptamers, CLIPs to inhibit RAGE signal transduction in mammalian cells.

(2013) PLoS One 8

PubMed: 23785412 | PubMedCentral: PMC3681763 | DOI: 10.1371/journal.pone.0065180

The structure of the second docking partner, PA #103, was based on E.coli Thioredoxin coordinates (PDB entry 2TRX [64] ) [40] .

The protein aptamer sequence, containing an N-terminal His 6 tag, peptide insert and scaffold mutations, was aligned with the wild type E.coli Thioredoxin structure (PDB code 2TRX, A-chain).

Publication Year: 2013


MISTIC: Mutual information server to infer coevolution.

(2013) Nucleic Acids Res 41

PubMed: 23716641 | PubMedCentral: PMC3692073 | DOI: 10.1093/nar/gkt427

Panel ( B ) Distance network of the reference structure (PDB code: 2trx).

Right: ribbon representation of the reference structure (PDB code: 2trx) colored as the network style (conservation).

( B ): ribbon representation of the reference structure (PDB code: 2trx) colored as the network style (cMI score).

The reference sequence and structure were set as THIO_ECOLI and PDB code 2trx.

Publication Year: 2013


An extended active-site motif controls the reactivity of the thioredoxin fold.

(2014) J Biol Chem 289

PubMed: 24469455 | PubMedCentral: PMC3961690 | DOI: 10.1074/jbc.M113.513457

The following PDB entries were used: E. coli thioredoxin ( 2TRX ( 48 )), E. coli cDsbD ( 2FWF ( 29 )), E. coli DsbA ( 1A2L ( 49 )), Bacillus subtilis BdbD ( 3EU3 ( 50 )), human protein-disulfide isome... ase ( 3UEM ( 51 )), human Trx1 ( 1TRS ( 52 )), E. coli CcmG ( 2B1K ( 53 )), B. subtilis ResA ( 1SU9 ( 54 )), B. subtilis StoA ( 3ERW ( 55 )), E. coli DsbC ( 1EEJ ( 56 )), and E. coli DsbG ( 1V57 ( 57 )).

Publication Year: 2014


A high-performance thioredoxin-based scaffold for peptide immunogen construction: proof-of-concept testing with a human papillomavirus epitope.

(2014) Sci Rep 4

PubMed: 24751665 | PubMedCentral: PMC3994442 | DOI: 10.1038/srep04729

The 3D structure of E. coli thioredoxin (PDB accession code: 2trx) is shown on the right with the two Cys residues of the redox active/display site represented in a ball and stick format.

Publication Year: 2014


Structural insight into substrate recognition by the endoplasmic reticulum folding-sensor enzyme: crystal structure of third thioredoxin-like domain of UDP-glucose:glycoprotein glucosyltransferase.

(2014) Sci Rep 4

PubMed: 25471383 | PubMedCentral: PMC4255179 | DOI: 10.1038/srep07322

Compared with the crystal structure of the E. coli thioredoxin trxA 28 (PDB code: 2TRX; Supplemental Fig.

Publication Year: 2014


A PDB-wide, evolution-based assessment of protein-protein interfaces.

(2014) BMC Struct Biol 14

PubMed: 25326082 | PubMedCentral: PMC4274722 | DOI: 10.1186/s12900-014-0022-0

Interface 1 of entry 2trx ( E.coli thioredoxin) fetched in PyMOL with the EPPIC Interface Loader plugin and displayed in hybrid mode (surface color-mapped by sequence entropy for one interface partner... and cartoon for the other partner).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4482675

Protein images were produced using PyMol and PDB entry 4AOU [ 24 ] and 2TRX [ 25 ].

Publication Year: 2015