1TSR

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 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.

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.

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.

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.

, ΔΔ G , of key residues identified from the p53 core domain (PDB: 1TSR).

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).

Superimposition of the p53–DNA complex (1tsr) onto the p53–ASPP2 protein–protein complex (1ycs).

( 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).

The search model was chain A (DNA-free) of the wild-type p53DBD structure (PDB code 1tsr ).

Crystal structure (codons 96 to 289), b chain of 1TSR [ 6 ] is used for the native state of the p53 DBC domain.

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).

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.

Modeled mutant proteins were produced in silico using the B chain of the wildtype p53 core domain crystal structure (PDB ID: 1TSR) [33] .

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 .

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 [46] .

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).

Methods System preparation The coordinates for the starting structure were obtained from the wild-type p53 coordinates of chain B in pdbID 1TSR [4] .

The view was created from PDB entry: 1TSR using the PyMOL software.

Materials and Methods Generation of the mutated structure Initial atomic coordinates for the DNA-bound WT p53 were obtained from the crystal structure [6] 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).

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).

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.

The crystal structure of the human p53 core domain (chain A of PDB ID 2AC0 or 1TSR) was used as a search model.

The spatial conformation of “LTIITL” in the crystal structure of a p53 tumor suppressor-DNA complex (PDB-id: 1TSR) is displayed in ( Figure 1A ).

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).

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).

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).