Citations in PubMed

Primary Citation PubMed: 8023157 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

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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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.

Publication Year: 2007


Stability of the core domain of p53: insights from computer simulations.

(2008) BMC Bioinformatics 9 Suppl 1

PubMed: 18315848 | PubMedCentral: PMC2259418 | DOI: 10.1186/1471-2105-9-S1-S17

Methods The initial structure of monomeric p53 core domain was taken from the crystal structure of p53 bound to DNA (RCSB entry 1TUP resolved at 2.2 Å; [ 20 ]); the structures of p63 and p73 w... re modeled based on the homology with the p53 monomer (sequence similarity to p63 and p73 is 77% and 75% respectively while identity is ~60%).

Publication Year: 2008


Molecular screening of compounds to the predicted Protein-Protein Interaction site of Rb1-E7 with p53- E6 in HPV.

(2012) Bioinformation 8

PubMed: 22829740 | PubMedCentral: PMC3400986 | DOI: 10.6026/97320630008607

Docking results : All the 88 natural compounds listed from the thorough literature survey were docked against E6 (PDB ID: 1VZN), p53 (PDB ID: 1TUP), Rb1 (PDB ID: 1AD6), E7 (PDB ID: 2B9D) at the specif... c sites of interaction predicted from SHARP2 results.

Docking studies : The selected compounds were docked against E6 (PDB ID: 1VZN), p53 (PDB ID: 1TUP), Rb1 (PDB ID: 1AD6), E7 (PDB ID: 2B9D), using Molegro Virtual Docker (MVD) [ 22 ].

Publication Year: 2012


Synergy of peptide and sugar in O-GlcNAcase substrate recognition.

(2012) Chem Biol 19

PubMed: 22365600 | PubMedCentral: PMC3476531 | DOI: 10.1016/j.chembiol.2012.01.011

Figure 2 Comparison of Glycopeptide Binding with the Native p53 Conformation and Inhibitor Complexes (A) Superposition of the p53-derived glycopeptide structure as observed in the complex with... Cp OGA D298N (orange and pink sticks) with the corresponding region of the p53 DNA binding domain crystal structure ( Cho et al., 1994 ) (blue sticks and cartoon; Protein Data Bank ID 1tup ).

Publication Year: 2012


The rebel angel: mutant p53 as the driving oncogene in breast cancer.

(2012) Carcinogenesis 33

PubMed: 22822097 | PubMedCentral: PMC3483014 | DOI: 10.1093/carcin/bgs232

Derived from Protein Data Bank (PDB) ID: 1TUP ( 33 ).

Publication Year: 2012


Variation in the mechanical unfolding pathway of p53DBD induced by interaction with p53 N-terminal region or DNA.

(2012) PLoS One 7

PubMed: 23145047 | PubMedCentral: PMC3493487 | DOI: 10.1371/journal.pone.0049003

The lower portion is the crystal structure of p53DBD(94–312)-DNA complex, PDB code 1TUP.

Publication Year: 2012


p28, a first in class peptide inhibitor of cop1 binding to p53.

(2013) Br J Cancer 108

PubMed: 23736031 | PubMedCentral: PMC3694247 | DOI: 10.1038/bjc.2013.266

Configurations for azurin and the DBD of p53 were taken from 1E5Z and 1TUP of PDB files, respectively.

Publication Year: 2013


Defining the structural origin of the substrate sequence independence of O-GlcNAcase using a combination of molecular docking and dynamics simulation.

(2014) Glycobiology 24

PubMed: 24134879 | PubMedCentral: PMC3854502 | DOI: 10.1093/glycob/cwt094

In addition, p53 (PDBid 1TUP) ( Cho et al. 1994 ) is the only structurally characterized protein where the O-GlcNAcylation site is positioned in a fully defined loop, thus allowing us to further compa... e our results ( Schimpl et al. 2012 ).

A comparison, of the crystallographic and MD-derived conformations of the p53 glycopeptides with the crystal structure of the full-length p53 protein (PDBid 1TUP) ( Cho et al. 1994 ), indicated that the W146 orientation from the MD results was in good agreement with the conformation seen in the intact p53 protein (Figure 2 ).

Ribbon representation of both, the most populated p53′ glycopeptide (blue) and the p53 glycopeptide from the Cp OGA complex 2YDR (yellow), were aligned onto the corresponding sequence (Leu 145 to Gly 151) in the p53 protein crystal (PDBid 1TUP) (grey).

This flexibility is also thought to occur in the region spanning the sites of known O-GlcNAcylated proteins, and as such there are currently no protein structures available, with the exception of p53 (PDbid 1TUP), where these regions are fully defined ( Schimpl et al. 2012 ).

Publication Year: 2014