Primary Citation PubMed: 8023157
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Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.
(2006) Nucleic Acids Res 34
PubMed: 16522644 | PubMedCentral: PMC1390679 | DOI: 10.1093/nar/gkj518
Figure 3 Representation of the DBD of p53 (PDB ID 1tsr, chain B), color-coded by GV values with the following cutoffs: GV = 0, red; 0 < GV < 61.3, orange; GV > 61.3, grey.
The X-ray solved structure of the DBD of human p53 [PDB ( 24 ) id 1tsr, chain B] was also input.
Publication Year: 2006
Energetics of protein-DNA interactions.
(2007) Nucleic Acids Res 35
PubMed: 17259221 | PubMedCentral: PMC1851630 | DOI: 10.1093/nar/gkl1103
The set then contains the following 30 structures: 1aay, 1apl, 1az0, 1azp, 1bc7, 1bhm, 1bp7, 1ca5, 1cdw, 1cma, 1cw0, 1ecr, 1efa, 1glu, 1hcq, 1hcr, 1ihf, 1ipp, 1lmb, 1mdy, 1nfk, 1oct, 1par, 1pue, 1qrv,... 1run, 1tro, 1tsr, 1ysa and 1ytf.
Because missing side-chains in the structure do not allow an energy calculation on the structure in AMBER, 13 structures were removed for the AMBER calculations (1apl, 1az0, 1bhm, 1efa, 1hcq, 1ihf, 1ipp, 1nfk, 1oct, 1par, 1qrv, 1tro and 1tsr).
Publication Year: 2007
Relating destabilizing regions to known functional sites in proteins.
(2007) BMC Bioinformatics 8
PubMed: 17470296 | PubMedCentral: PMC1890302 | DOI: 10.1186/1471-2105-8-141
Pdb id a Holo-pdb ids b N res c F res d ASA e F ASA f Cleft g Small 1e1a 13 4.2 272 2.1 T 1e3f 1bm7 , 1e4h , 1e5a , 1eta , 1tha 8 6.9 193 1.0 T 1gu7 1guf , 1n9g 31 8.5 1158 3.7 T 1gud 1rpj 24 8.3 976 ... .4 T 1gus 1gug , 1gun , 1guo 4 6.0 119 0.9 F 1gus h 1gug , 1gun , 1guo 14 20.9 110 0.8 F 1gxy 1og1 , 1og3 , 1og4 24 10.8 947 8.7 T 1hf8 1hfa , 1hg2 , 1hg5 4 1.5 329 1.4 F 1hhq 1hiy , 1b4s , 1b99 , 1bux 17 11.3 1006 2.8 T 1is5 1is3 , 1is4 , 1is6 22 16.4 663 3.0 T 1jcf 1jcg 34 10.1 820 5.6 F 1odl 1odi , 1odj 25 10.7 339 0.8 T 1ofn 1oi6 15 7.4 669 4.0 T 1tm2 1tjy 19 6.1 437 3.2 T 1upq 1upr 12 11.2 783 11.9 T 1usg 1usk , 1usi 15 4.3 268 1.0 T 1usl 2bes , 2bet 18 11.5 505 3.9 T 1w1h 1w1d , 1w1g 10 6.6 560 6.2 T 1w2i 1w2i 8 8.9 450 5.0 F 1w37 1w3i , 1w3n , 1w3t 12 4.1 107 0.3 T 1y2t 1y2x , 1y2w 27 19.0 1191 5.6 F Polysaccharide 1nof 12 3.1 471 3.2 T 1o88 15 4.2 472 3.5 T 1ob0 1e3z 41 8.5 1572 8.9 T 1ogb 1e6n , 1e6r , 1h0g , 1h0i , 1ogg 16 3.2 565 1.5 T 1qhz 1qi2 , 8a3h , 4a3h , 1e5j , 1qi0 14 4.6 590 5.2 T 1qjv 10 2.9 265 1.8 T 1uuq 1uz4 16 3.9 256 1.7 T 1w0n 1ux7 8 6.7 642 11.2 T 1w6z 1sf7 , 1sfb , 1sfg 20 15.5 891 13.6 T 1w9s 1w9t , 1w9w 12 9.0 376 5.9 F Peptide 1c7k 9 6.8 275 4.2 T 1e5t 1e8m , 1e8n , 1o6g , 1qfs , 1uop 18 2.5 485 1.7 T 1ea7 7 2.3 97 0.9 T 1gt9 1gtj , 1gtl 21 5.9 450 3.4 F 1kl4 1hqq , 1kl3 , 1kl5 , 1rsu 17 14.2 854 4.2 T 1oes 1g1f , 1g1g , 1g1h , 1ptt , 1ptu 16 5.7 885 6.6 T 1r29 1r2b 29 23.8 1760 13.8 F Protein 1e3f 1qab , 1rlb 15 13.0 971 5.0 F 1e6l 1bdj 10 7.9 775 11.7 F 1e6l 1a0o , 1eay , 1ffg , 1ffs , 1ffw 15 11.8 1212 18.4 T 1eao 1e50 , 1h9d 26 22.8 1819 28.2 F 1f2x 12 9.5 604 5.2 F 1gcp 1gcq 21 31.3 1405 33.2 F 1gqv 2bex 36 26.7 2246 28.9 F 1obq 1gka 22 12.2 1023 6.1 T 1sif 1cmx , 1fxt , 1nbf , 1otr , 1q5w , 1s1q , 1uzx 14 19.7 937 21.7 T 1tgr 1h59 15 28.8 1236 29.5 T 1uns 1jck 19 8.1 1620 13.5 F 1uns 1jwm 20 8.5 1386 11.6 F 1uol 1gzh , 1kzy 18 9.2 1301 13.1 F 1uq4 2aai 42 16.0 2796 21.6 F 1w53 12 14.3 770 8.8 T Nucleic acid 1e7l 8 5.1 352 2.0 T 1eao 1h9d , 1hjb 18 15.8 1375 21.3 F 1gqv 1hi3 , 1hi4 , 1hi5 9 6.7 245 3.2 T 1gv2 1h88 , 1h89 , 1mse 30 29.1 2289 30.2 T 1o7i 5 4.3 497 7.4 F 1okb 1emh , 1emj , 1q3f , 1ssp , 2ssp , 4skn 30 13.5 1539 15.0 T 1uol 1tsr , 1tup 19 9.7 1229 12.4 F 1uq4 1apg , 1br5 17 6.5 364 2.8 T 1utx 10 15.2 691 9.0 F 1vyi 10 9.0 1009 15.0 F Lipid 1obq 1h91 , 1i4u , 1s2p , 1s44 21 11.6 350 2.1 T 1qmd 14 3.8 465 2.9 F Metal 1e6l 1chn , 1ymv 7 5.5 350 5.3 T 1qmd 1kho 6 1.6 67 0.4 T Peptide-Protein 1mix 1mk7 , 1mk9 26 12.6 1526 11.9 F Small-Metal 1h1y 19 8.6 365 2.2 T 1h6l 2poo , 1h6l 16 4.5 627 4.4 T 1oid 1ho5 , 1hp1 , 1hpu 19 3.6 872 3.9 F Polysaccharide-Metal 1gkb 1bxh , 1cjp , 1c57 , 1ces , 1dq1 , 1gkb , 3cna , 3enr 19 8.0 586 1.8 F Lipid-Metal 1umv 1pob , 1umv , 1c1j 17 13.9 492 3.8 T Protein-Metal 1o6v 1o6s 49 10.6 2224 11.3 F Properties of known binding sites of the dataset proteins.
PI2PE: protein interface/interior prediction engine.
PubMed: 17526530 | PubMedCentral: PMC1933225 | DOI: 10.1093/nar/gkm231
Predictions were made on the unbound structure of p53 (2fej) but are displayed on the bound ( A ) protein–protein and ( B ) protein–DNA (1tsr) complexes.
Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements.
PubMed: 17986463 | PubMedCentral: PMC2190717 | DOI: 10.1093/nar/gkm890
Tetrameric structural models were assembled, based on available X-ray structures of trimeric p53–DNA (PDB code 1tsr) ( 8 ) and dimeric p53–DNA ( 9 , 10 ) complexes.
Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.
(2008) PLoS Comput Biol 4
PubMed: 18654622 | PubMedCentral: PMC2447880 | DOI: 10.1371/journal.pcbi.1000135
, ΔΔ G , of key residues identified from the p53 core domain (PDB: 1TSR).
t001 Table 1 Prediction of nsSNPs in the core domain of p53 (PDB: 1TSR) by Bongo Mutant categories nsSNP ΔΔ G a (kcal/mol) Crystal structure Prediction of Bongo Prediction of PolyPhen No structural effects R273H 0.09  2BIM Benign Probably damaging Weakly/locally destabilising G245S 1.22  – b Damaging Probably damaging R249S 1.69  2BIO Damaging Probably damaging R248A 1–2  – Damaging Probably damaging Highly destabilising/global unfolding C242S >2  – Damaging Probably damaging H168R 2.75  2BIN Damaging Probably damaging V143A 3.34  – Damaging Benign I195T >2  – Damaging Probably damaging a The free energy difference (destabilisation) compared to wild-type p53 core domain.
When the structure 1TSR in PDB was used as a calibration model, Bongo identified all mutations except R273H as causing structural effects in the p53 core domain ( Table 1 ), which corresponds well with experimental data described in the literature.
Publication Year: 2008
Insights into protein-DNA interactions through structure network analysis.
PubMed: 18773096 | PubMedCentral: PMC2518215 | DOI: 10.1371/journal.pcbi.1000170
Class 1 Class 2 Class 3 Class 4 Class 5 Class 6 Class 7 P-p clusters only P-S clusters only P-B clusters only P-p and P-S clusters (no P-B clusters) P-S and P-B clusters (no P-p clusters) P-p and P-B ... lusters (no P-S clusters) P-p, P-S, and P-B clusters are present Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping P-p, P-B, and P-S clusters Non-overlapping P-p, P-B, and P-S clusters P-p and P-S clusters overlap but not P-B clusters P-S and P-B clusters overlap but not P-p clusters P-p and P-B clusters overlap but not P-S clusters P-P, P-B and P-S clusters occur separately β-Hairpin β-Hairpin Zinc coordinating group Enzymes β-Hairpin β-Hairpin Other α-helices Others Helix turn helix – β-Hairpin β-Sheet Enzymes β-Hairpin 1cma- a 1azp- 1zaa- 1a31- 1ecr- 1bnz- 1ckt- 1ramA 1apl- 1bdt- 1d3u- 1bss- 1ihf- a Enzymes 1bf4- 1a35- 1xbr- a β-Sheet 1vkx- 1lli- Enzymes 1tgh- 1ipp- β-Sheet 7ice- Enzymes 1bhm- a Enzymes 1c9bB Zipper type Others 1cyq- Enzymes Helix turn helix 1vol- Helix turn helix 2dnj- 1dnk- 1bnk- 1cdw- 1an4- 1a3qA 1dctA 2bdp- 1tc3- Enzymes 3orc- 2rve- 1t7pA 1bpx- Enzymes 1hlo- a 1bf5-* 1rv5- 3ktq- 1a74- a Other α-helices 3bam- 1qss- 10mh- 1nfkA 4skn- Helix turn helix 1ssp- 1skn- Helix turn helix 1qsy- 1clq- Zinc coordinating group 5mht- 1fjl- a 1vas- Zipper type 6pax- 2bpf- 1pvi- a 1a1g- Helix turn helix Zinc coordinating group 3pvi- 1ysa- a Other α-helices 2ktq- 1tau- 1aay-* 1gdt- a 1cit- Helix turn helix 1b3t- a 2ssp- 2pvi- 1d66-* 1ignA a 1fok- Zinc coordinating group 4ktq- Other α-helices 1ubd-* 1rpe- 1hcr- a 1lat- Helix turn helix 1qrv- 1zme- 6cro- 1mnm- a 1akh- Zipper type Zinc coordinating group 1yrn- a 1hddC a 1an2- 2gli- a 3cro- a 1pdn- Zipper type Zinc coordinating group 3hddA 1a02- 1a6y- Other α-helices 1a0a- 1aoi- Zinc coordinating group 1glu- 1tsr- a 2nll- a These protein–DNA complexes are also present in DS3 (see Materials and Methods section).
Molecular interactions of ASPP1 and ASPP2 with the p53 protein family and the apoptotic promoters PUMA and Bax.
(2008) Nucleic Acids Res 36
PubMed: 18676979 | PubMedCentral: PMC2532732 | DOI: 10.1093/nar/gkn490
Superimposition of the p53–DNA complex (1tsr) onto the p53–ASPP2 protein–protein complex (1ycs).
Crystal structure of a p53 core tetramer bound to DNA.
(2009) Oncogene 28
PubMed: 18978813 | PubMedCentral: PMC2629805 | DOI: 10.1038/onc.2008.400
( e ) Close up view of the L1 loops from human (2OCJ, orange) and mouse (1HU8, red) p53DBD; human p53DBD (1TSR, yellow), human p53DBD dimer (2AC0, magenta), mouse p53DBD dimer (2GEQ, cyan) bound to DN... ; Cep-1 p53 ortholog (1T4W, blue), mouse p53DBD tetramer bound to DNA structure 1 (green) and mouse p53DBD tetramer bound to DNA structure 2 (light green).
Publication Year: 2009
Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 angstroms resolution.
(2008) Acta Crystallogr D Biol Crystallogr 64
PubMed: 18453682 | PubMedCentral: PMC2631104 | DOI: 10.1107/S0907444908003338
The search model was chain A (DNA-free) of the wild-type p53DBD structure (PDB code 1tsr ).
The crystal structure of wild-type p53DBD in complex with DNA (PDB code 1tsr ) contains three chains.
When the p53DBD(R282Q) structure is superimposed with the wild type (PDB code 1tsr ), the r.m.s.d. for all C α atoms is 0.57 Å for chain A , 0.58 Å for chain B and 0.59 Å for chain C and the most noticeable deviations are observed in the L1, L2 and L3 loops and a turn between the S7 and S8 strands (Fig. 3 ▶ a ).
( a ) The C α trace of p53DBD(R282Q) is shown in magenta and is superimposed with DNA-free (PDB code 1tsr ; chain A , yellow) and DNA-bound (chain B , cyan; chain C , blue) wild-type protein.
On the basis of the crystal structure of human p53DBD in complex with a consensus DNA (PDB code 1tsr ), Arg248 and Arg273 directly contact the DNA, while the others appear to play a role in stabilizing the structure of the DNA-binding surface of p53DBD (Cho et al. , 1994 ▶ ).
Structural and functional implications of p53 missense cancer mutations.
(2009) PMC Biophys 2
PubMed: 19558684 | PubMedCentral: PMC2709103 | DOI: 10.1186/1757-5036-2-5
Crystal structure (codons 96 to 289), b chain of 1TSR [ 6 ] is used for the native state of the p53 DBC domain.
Unfoldomics of human diseases: linking protein intrinsic disorder with diseases.
(2009) BMC Genomics 10 Suppl 1
PubMed: 19594884 | PubMedCentral: PMC2709268 | DOI: 10.1186/1471-2164-10-S1-S7
The Protein Data Bank IDs and partner names for the structures (from upper left, clockwise) are as follows: ( 1tsr DNA), ( 1gzh 53BP1), ( 1q2d gcn5), ( 3sak p53 (tet dom)), ( 1xqh set9), ( 1h26 cyclin... ), ( 1ma3 sirtuin), ( 1jsp CBP bromo domain), ( 1dt7 s100bb), ( 2h1l sv40 Large T antigen), ( 1ycs 53BP2), ( 2gs0 PH), ( 1ycr MDM2), and ( 2b3g rpa70).
Investigation and prediction of the severity of p53 mutants using parameters from structural calculations.
(2009) FEBS J 276
PubMed: 19558493 | PubMedCentral: PMC2730554 | DOI: 10.1111/j.1742-4658.2009.07124.x
Structural modelling and energy calculations The three-dimensional structure of p53 was taken from the PDB entry 1tsr chain 1 [ 25 ] in the RCSB protein data bank ( http://www.pdb.org ), as a basis fo... all measurements and simulations.
The structure is based on the 1tsr crystal structure of p53.
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.
(2009) PLoS Comput Biol 5
PubMed: 19756158 | PubMedCentral: PMC2742196 | DOI: 10.1371/journal.pcbi.1000498
Modeled mutant proteins were produced in silico using the B chain of the wildtype p53 core domain crystal structure (PDB ID: 1TSR)  .
Integration of open access literature into the RCSB Protein Data Bank using BioLit.
(2010) BMC Bioinformatics 11
PubMed: 20429930 | PubMedCentral: PMC2880030 | DOI: 10.1186/1471-2105-11-220
of Articles 1JJ2 Large Ribosomal Subunit 27 1J5E 30S Ribosomal Subunit 19 1FFK Large Ribosomal Subunit 19 1LMB Lambda Repressor 19 1AAY Zinc Finger 17 1TSR P53 16 1F88 Rhodopsin 15 1BRS Barnase/Barsta... complex 14 The open access literature for RCSB PDB entries is available from the Literature tab for each structure entry at http://www.rcsb.org .
Publication Year: 2010
Lysine120 interactions with p53 response elements can allosterically direct p53 organization.
(2010) PLoS Comput Biol 6
PubMed: 20700496 | PubMedCentral: PMC2916859 | DOI: 10.1371/journal.pcbi.1000878
Methods MD simulation protocol MD simulations were performed on 12 p53 dimer-DNA half site complexes constructed based on the p53-DNA crystal structure with the PDB code 1tsr  .
Modeling of p53 dimer-DNA complexes for each p53-RE half site The p53 core domain dimer-half site DNA complex was generated based on the crystal structure template (PDB code: 1tsr)  , as described earlier  ,  .
M-ORBIS: mapping of molecular binding sites and surfaces.
(2011) Nucleic Acids Res 39
PubMed: 20813758 | PubMedCentral: PMC3017595 | DOI: 10.1093/nar/gkq736
From top left to bottom right, the cartography of proteins: ribonuclease inhibitor (1dfj), ferrodoxin-nadp reductase (1ewy); neuraminidase (3b7e); cAMP-dependent kinase (1ydr); p53 tumor suppressor (1... sr); neurotoxin bont/A (1xtg); acetylcholinesterase (1fss); guanine nucleotide-binding protein G(i) (1bof).
Publication Year: 2011
Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants.
(2011) PLoS Comput Biol 7
PubMed: 22028641 | PubMedCentral: PMC3197647 | DOI: 10.1371/journal.pcbi.1002238
Methods System preparation The coordinates for the starting structure were obtained from the wild-type p53 coordinates of chain B in pdbID 1TSR  .
Proteasomal degradation of p53 by human papillomavirus E6 oncoprotein relies on the structural integrity of p53 core domain.
(2011) PLoS One 6
PubMed: 22046250 | PubMedCentral: PMC3203139 | DOI: 10.1371/journal.pone.0025981
The view was created from PDB entry: 1TSR using the PyMOL software.
Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: comparing the wild type to the R248Q mutant.
PubMed: 22110706 | PubMedCentral: PMC3218007 | DOI: 10.1371/journal.pone.0027651
Materials and Methods Generation of the mutated structure Initial atomic coordinates for the DNA-bound WT p53 were obtained from the crystal structure  of the DBD in complex with a 21 base-pair DNA... duplex ( 5′-ATATTTGGGCAAGTCTAGGAA-3′ ), available from the Protein Data Bank (PDB ID: 1TSR; chain B).
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.
(2012) BMC Bioinformatics 13
PubMed: 22800292 | PubMedCentral: PMC3472317 | DOI: 10.1186/1471-2105-13-165
Table 1 Representatives for previous families 54 existing families (Thornton classification) representatives were selected and were validated using Jack-knifing Group Families Representative(s) HTH ... 000a0; Cro & repressor 1LMB Homeodomain 1FJL, 1HDD, 6PAX LacI repressor 1WET Endonuclease Fok1 1FOK Gamma Delta resolvase 1GDT Hin recombinase 1HCR RAP1 family 1IGN Prd paired domain 1PDN Tc3 transposase 1TC3 Trp repressor 1TRR Diptheria tox repressor 1DDN Transcription factor IIB 1D3U Interferon regulatory 2IRF Catabolite gene activator protein 1RUO Transcription factor 1CF7, 3HTS Ets domain 1BC8 Zinc Co-ordinating β-β-α zinc finger 1ZAA Harmone Nuclear Receptor 2NLL Loop sheet helix 1TSR GAL4 type 1ZME Zipper type Leucine Zipper 1YSA Helix loop helix 1AN2 Other-α Helix Pappilomavirus 1 E2 2BOP Histone 1AOI EBNA1 nuclear protein 1B3T Skn-1 transcription factor 1SKN Cre Recombinase 1CRX High Mobility Group 1QRV MADS box 1MNM β-Sheet TATA box binding 1YTB β-Hairpin/Ribbon MetJ repressor 1CMA Tus replication terminator 1ECR Integration host factor 1IHF Transcription Factor T-domain 1XBR Hyperthermophile DNA 1AZP Arc repressor 1PAR Other ReI homology 1SVC Stat protein 1BF5 Enzyme Methyltransferase 6MHT Endonuclease PvuII 3PVI Endonuclease ecorV 1RVA Endonuclease ecorI 1QPS Endonuclease BamHI 3BAM Enonuclease V 1VAS Dnase I 2DNJ DNA mismatch endonuclease 1CW0 DNA polymerase β 1BPY DNA Polymerase I 2BDP DNA Polymerase T7 1T7P,1CLQ HIV Reverse Transcriptase 2HMI Uracil DNA glycosylase 1SSP 3-Methyladenine DNA glycosylase 1BNK Homing endonuclease 1A73, 1BP7 TopoisomeraseI 1A31 For all the 59 selected representatives, PSI-BLAST profiles were again built against dummy database using the earlier profile creation parameters (as described in Methods).
Publication Year: 2012
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53.
(2013) Nat Commun 4
PubMed: 23360998 | PubMedCentral: PMC3562459 | DOI: 10.1038/ncomms2361
Blind docking of known p53 reactivation compounds onto the entire protein surface of the human p53 core domain crystal structure PDB ID 1TSR chain B (1TSR-B) 33 indicated that none of the compounds bo... nd in close proximity to any cysteine, including those in the L1/S3 pocket ( Supplementary Fig.
In contrast, neither Cys124 nor any other cysteine in the original PDB crystal structure 1TSR-B 33 was identified as a druggable site by FTMap.
In the crystal structures of the human p53 core DNA-binding domain (PDB IDs 1TSR 33 , 2OCJ 34 ), Cys124 is partially occluded and the putative L1/S3 reactivation pocket is not readily accessible to small molecules much larger than water.
In sharp contrast, in the p53 core domain crystal structure 1TSR-B the Cys124 side chain SASA was calculated to be only 0.43 Å 2 .
Methods MD simulations Wild-type p53 MD simulations were performed using crystal structure 1TSR-B 33 for the initial coordinates.
( a , b ) All residues of the p53 core domain (1TSR-B 33 ) within 10 Å of Cys124 are shown in a surface representation coloured by atom type: cyan, C; blue, N; red, O; yellow, S. ( a ) Cys124 is initially occluded in the wt crystal structure.
Publication Year: 2013
Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions.
(2013) Nucleic Acids Res 41
PubMed: 23863845 | PubMedCentral: PMC3794590 | DOI: 10.1093/nar/gkt630
The crystal structure of the human p53 core domain (chain A of PDB ID 2AC0 or 1TSR) was used as a search model.
PPS: A computing engine to find Palindromes in all Protein sequences.
(2014) Bioinformation 10
PubMed: 24516327 | PubMedCentral: PMC3916820 | DOI: 10.6026/97320630010048
The spatial conformation of “LTIITL” in the crystal structure of a p53 tumor suppressor-DNA complex (PDB-id: 1TSR) is displayed in ( Figure 1A ).
Publication Year: 2014
PubMed ID is not available.
Published in 2014
Starting with the p53–DNA complex (top, left, magenta protein, blue DNA), and moving in a clockwise direction, the Protein Data Bank 147 IDs and partner names are given as follows for the 14 c... mplexes: (1tsr – DNA), (1gzh – 53BP1), (1q2d – gcn5), (3sak – p53 (tetramerization domain)), (1xqh – set9), (1h26 – cyclin A), (1ma3 – sirtuin), (1jsp – CBP bromo domain), (1dt7 – s100ββ), (2h1l – sv40 Large T antigen), (1ycs – 53BP2), (2gs0 – PH), (1ycr – MDM2), and (2b3g – RPA70).
Iron metabolism regulates p53 signaling through direct heme-p53 interaction and modulation of p53 localization, stability, and function.
(2014) Cell Rep 7
PubMed: 24685134 | PubMedCentral: PMC4219651 | DOI: 10.1016/j.celrep.2014.02.042
Coordinates of the p53-DNA complex were extracted from the Protein Data Bank (PDB 1TSR) ( Cho et al., 1994 ) and visualized on PyMOL (DeLano Scientific).
(C) A close-up view of the C 275 and C 277 residues of human p53 in the p53 core domain-DNA ( Cho et al., 1994 ) (derived from PDB 1TSR).
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.
(2005) Nucleic Acids Res 33
PubMed: 15673715 | PubMedCentral: PMC548349 | DOI: 10.1093/nar/gki204
Non-TF/DNA refers to 27 non-transcription factor/DNA complexes (including 1mse, 1tro, 1ca5, 2ezd, 1lcc, 1cjg, 1gcc, 1azp, 1az0, 1b69, 1tf3, 1bhm, 1ecr, 1cw0, 1hcr, 1yui, 1sx9, 7icr, 1qaa, 1jey, 1nk2, ... tau, 5gat, 1qrv, 1a73, 2gat and 1j1v), TF/DNA refers to remaining 21 transcription factor complexes (including 1lmb, 1cma, 1apl, 1par, 1run, 1glu, 1nfk, 1efa, 1mdy, 1tsr, 1ipp, 1ytf, 1vkx, 1oct, 1ihf, 1bc7, 1aay, 1cez, 1yrn, 1ysa and 1b3t).
Table 1 Data set of protein–DNA complexes Structural set (141 complexes) 1a02 1a0a 1a1g 1a1h 1a1k 1a3q 1akh 1am9 1an2 1an4 1apl 1au7 1b01 1b3t 1b72 1b8i 1bc8 1bdt 1bf5 1bl0 1by4 1c0w 1c9b 1cdw 1cez 1cf7 1cgp 1cit 1d3u 1d5y 1ddn 1dh3 1du0 1dux 1e3o 1ea4 1efa 1egw 1f2i 1f5t 1fjl 1fos 1fzp 1g2f 1gd2 1gji 1gt0 1gu4 1gu5 1gxp 1h6f 1h8a 1h9d 1h9t 1hbx 1hcq 1hlo 1hlz 1hw2 1hwt 1ic8 1if1 1ig7 1ign 1imh 1io4 1j59 1je8 1jfi 1jgg 1jj4 1jk1 1jk2 1jnm 1jt0 1k6o 1k78 1k79 1k7a 1kb2 1kb4 1kb6 1ku7 1l3l 1lat 1lb2 1le5 1le9 1llm 1lmb 1lq1 1mdy 1mhd 1mjm 1mjo 1mm8 1mnm 1mnn 1mur 1n6j 1ngm 1nkp 1nvp 1nwq 1oct 1odh 1owf 1p47 1p7h 1pdn 1per 1pp7 1pp8 1pue 1puf 1pyi 1pzu 1r0o 1r4o 1r4r 1ram 1rio 1rpe 1run 1skn 1tf6 1tgh 1tsr 1ubd 1yrn 1ysa 1ytb 1ytf 2cgp 2drp 2gli 2hap 2hdd 2or1 6cro 6pax Table 2 Recognition accuracy for specific interactions between TFs and native bound DNA sequences Accuracy Top 1(%) Top 10(%) Top 20(%) Top 1(%) Top 5(%) Whole structural set 39.7 70.2 77.3 79.4 90.1 α-Helix a 26.3 54.4 63.2 66.7 82.5 α-Helix + β-strand a 49.4 79.2 85.7 87.0 94.8 a α-helix and β-strand refer to the secondary structures of DNA-binding sites.
Publication Year: 2005
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