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PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

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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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Sequence variation in ligand binding sites in proteins.

(2005) BMC Bioinformatics 6

PubMed: 16194281 | PubMedCentral: PMC1261162 | DOI: 10.1186/1471-2105-6-240

Rendered with PyMOL from PDB entry 1A1I .

Publication Year: 2005

Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.

(2007) Nucleic Acids Res 35

PubMed: 17264128 | PubMedCentral: PMC1851644 | DOI: 10.1093/nar/gkl1155

C 2 H 2 ZF-DNA PDB files PDB code Chains Description Res (Å) Topology a 1llm C,D Zif268-GCN4 (dimer) 1.5 2_3:3_2 1aay A Zif268 1.6 3_2_1 1a1f, 1a1g, 1a1h, 1a1i, 1a1j, 1a1k, 1a1l A Zif268 (Fn1 ... utants) 1.6 3_2_1 1jk1, 1jk2 A Zif268 (Fn1 D20A) 1.9 3_2_1 1zaa C Zif268 2.1 3_2_1 1mey C,F Designed 2.2 3_2_1 1g2d, 1g2f C,F Designed 2.2 3_2_1 1p47 A,B Zif268 tandem 2.2 3_2_1 3_2_1 1f2i G,H,I,J,K,L Zif268-extension (dimer) 2.4 2_1:1_2 1ubd C YY1 (Yin Yang 1) 2.5 4_3_2_1 2gli A GLI (glioblastoma) 2.6 5_4_3_2_1 2drp A,D Tramtrack 2.8 2_1 1tf6 A,D TFIIIA n/a (NMR) 6_5_4_3_2_1 a Topology description for the individual ZF domains; 3_2_1 indicates a polydactyl ZF protein with three ZF domains, 1 refers to the N-terminal ZF domain.

Publication Year: 2007

DNA conformations and their sequence preferences.

(2008) Nucleic Acids Res 36

PubMed: 18477633 | PubMedCentral: PMC2441783 | DOI: 10.1093/nar/gkn260

The PDB codes of the structures used in the analysis Structure Type PDB Codes Noncomplexed A-DNA ( 46 ) 118d, 137d, 138d, 160d, 1d78, 1d79, 1dnz, 1kgk, 1m77, 1ma8, 1mlx, 1nzg, 1vj4, 1xjx, 1z7i, 1zex, ... zey, 1zf1, 1zf6, 1zf8, 1zf9, 1zfa, 213d, 243d, 260d, 295d, 2d94, 317d, 338d, 344d, 345d, 348d, 349d, 368d, 369d, 370d, 371d, 395d, 396d, 399d, 414d, 440d, 9dna, dh010, adh012, adh034 Noncomplexed B-DNA ( 72 ) 122d, 123d, 158d, 183d, 196d, 1bd1, 1bna, 1cw9, 1d23, 1d3r, 1d49, 1d56, 1d61, 1d8g, 1d8x, 1dou, 1dpn, 1edr, 1ehv, 1en3, 1en8, 1en9, 1ene, 1enn, 1fq2, 1g75, 1i3t, 1ikk, 1j8l, 1jgr, 1l4j, 1l6b, 1m6g, 1n1o, 1nvn, 1nvy, 1p4y, 1p54, 1s23, 1s2r, 1sgs, 1sk5, 1ub8, 1ve8, 1zf0, 1zf3, 1zf4, 1zf5, 1zf7, 1zfb, 1zff, 1zfg, 232d, 251d, 2d25, 307d, 355d, 3dnb, 403d, 423d, 428d, 431d, 436d, 454d, 455d, 456d, 460d, 463d, 476d, 477d, 5dnb, 9bna DNA/drug and DNA/ protein complexes, Z-DNA, quadruplexes (329) 110d, 115d, 131d, 145d, 151d, 152d, 159d, 181d, 182d, 184d, 190d, 191d, 1a1g, 1a1h, 1a1i, 1a1k, 1a2e, 1a73, 1aay, 1ais, 1azp, 1b94, 1b97, 1bf4, 1bqj, 1brn, 1c8c, 1cdw, 1ckq, 1cl8, 1cn0, 1d02, 1d11, 1d14, 1d15, 1d21, 1d22, 1d2i, 1d32, 1d37, 1d38, 1d40, 1d41, 1d45, 1d48, 1d53, 1d54, 1d58, 1d67, 1d76, 1d90, 1d9r, 1da0, 1da2, 1da9, 1dc0, 1dc1, 1dcg, 1dcr, 1dcw, 1dfm, 1dj6, 1dl8, 1dn4, 1dn5, 1dn8, 1dnf, 1dp7, 1dsz, 1e3o, 1egw, 1em0, 1emh, 1eo4, 1eon, 1esg, 1eyu, 1f0v, 1fd5, 1fdg, 1fhz, 1fiu, 1fms, 1fn1, 1fn2, 1g2f, 1g9z, 1gtw, 1gu4, 1h6f, 1hcr, 1hlv, 1hwt, 1hzs, 1i0t, 1i3w, 1ick, 1ign, 1ih4, 1ih6, 1imr, 1ims, 1j59, 1j75, 1jb7, 1jes, 1jft, 1jh9, 1jk1, 1jk2, 1jpq, 1jtl, 1juc, 1jux, 1jx4, 1k3w, 1k3x, 1k9g, 1kbu, 1kci, 1kx3, 1kx5, 1l1h, 1l1t, 1l1z, 1l3l, 1l3s, 1l3t, 1l3u, 1l3v, 1lat, 1lau, 1ljx, 1llm, 1lmb, 1m07, 1m19, 1m3q, 1m5r, 1m69, 1m6f, 1mf5, 1mj2, 1mjm, 1mjo, 1mjq, 1mnn, 1mus, 1mw8, 1nh2, 1njw, 1njx, 1nk0, 1nk4, 1nk7, 1nk8, 1nk9, 1nkc, 1nke, 1nkp, 1nnj, 1nqs, 1nr8, 1nt8, 1nvp, 1o0k, 1omk, 1orn, 1p20, 1p3i, 1p3l, 1p71, 1per, 1pfe, 1ph4, 1ph6, 1ph8, 1pji, 1pjj, 1puf, 1pup, 1puy, 1q3f, 1qda, 1qn3, 1qn4, 1qn5, 1qn6, 1qn8, 1qn9, 1qna, 1qnb, 1qne, 1qum, 1qyk, 1qyl, 1qzg, 1r2z, 1r3z, 1r41, 1r68, 1rff, 1rh6, 1rnb, 1rpe, 1rqy, 1run, 1s1k, 1s1l, 1s32, 1ssp, 1suz, 1sx5, 1sxq, 1t9i, 1tdz, 1tez, 1tro, 1u1p, 1u1q, 1u1r, 1u4b, 1ue2, 1ue4, 1uhy, 1v3n, 1v3o, 1v3p, 1vzk, 1w0u, 1wd0, 1wte, 1wto, 1wtp, 1wtq, 1wtr, 1wtv, 1xa2, 1xam, 1xc9, 1xjv, 1xo0, 1xuw, 1xux, 1xvn, 1xvr, 1xyi, 1ytb, 1ytf, 1zez, 1zf2, 1zna, 200d, 210d, 211d, 212d, 215d, 221d, 224d, 234d, 235d, 236d, 241d, 242d, 244d, 245d, 254d, 258d, 276d, 277d, 278d, 279d, 284d, 288d, 292d, 293d, 2bdp, 2bop, 2cgp, 2crx, 2dcg, 2des, 2hap, 2hdd, 2nll, 2or1, 2pvi, 304d, 306d, 308d, 313d, 314d, 331d, 334d, 336d, 351d, 352d, 360d, 362d, 366d, 367d, 383d, 385d, 386d, 3bam, 3bdp, 3cro, 3crx, 3hts, 3pvi, 400d, 417d, 427d, 432d, 441d, 442d, 443d, 452d, 453d, 465d, 467d, 473d, 481d, 482d, 4bdp, adh013, zdf013, zdfb03, zdfb06 The DNA conformational space was investigated at the level of a dinucleotide unit with its 5′-end phosphate group removed; it was described by six backbone torsion angles between γ and δ + 1, plus two χ angles characterizing the glycosidic bond ( Figure 1 ).

Publication Year: 2008

Structural interpretation of protein-protein interaction network.

(2010) BMC Struct Biol 10 Suppl 1

PubMed: 20487511 | PubMedCentral: PMC2873827 | DOI: 10.1186/1472-6807-10-S1-S4

For the other three proteins – YBR160W, YML032C, and YDL020C – the PDB homologs are 3EZR chain A (62% identity), 1KN0 chain A (53% identity), and 1A1I chain A (43% identity), respectiv... ly.

Publication Year: 2010

Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes.

(2010) BMC Struct Biol 10

PubMed: 21106075 | PubMedCentral: PMC3002361 | DOI: 10.1186/1472-6807-10-42

PDB Code Aminoacid sequence at positions -1, 2, 3, 6 Kd (nM) Total Protein Flexibility (RMSF sum (nm)) Total Complex Flexibility (RMSF sum (nm)) 1A1F DSNR 0.019 7.18 9.49 1A1G DSNR 1.8 6.05 8.70 1A1I ... ADR 0.068 7.72 9.03 1A1J RADR 0.035 7.6 10.1 1A1K RADR 9.3 5.87 8.38 1A1L RDER (wild type) 5.6 6.10 7.97 1AAY RDER (wild type) 2.7 6.47 8.68 Correlation Log(Kd)/RMSF -0.92 -0.88 The complexes simulated, the dissociation constants, the total flexibility of each system evaluated as a sum of the Root Mean Square Fluctuations (RMSFs) of the proteins and of the complexes are indicated.

PDB Code Protein-Protein Protein-DNA DNA-DNA Total Stabilization Energy Intra-protein 1A1F -58,47 -414,60 -734,92 -1207,99 -513,38 1A1G -64,77 -432,7 -722,54 -1220,01 -390,68 1A1I -65,75 -433,5 -714,52 -1213,77 -367,53 1A1J -66,12 -438,35 -726,55 -1231,02 -440,24 1A1K -61,61 -423,81 -728,83 -1214,25 -137,19 1A1L -89,11 -501,37 -705,23 -1295,71 -210,41 1AAY -64,44 -432,67 -726,34 -1223,45 -342,07 Energetic contributions calculated according to the Energy Decomposition Method due to intraprotein, protein-DNA and intra-DNA contributions are indicated.

PDB Code Aminoacid sequence at positions -1, 2, 3, 6 Nucleotidic sequence at positions 8-11 Dissociation Constant (Kd, nM) 1A1F DSNR GACC 0.019 1A1G DSNR GCGT (wild type) 1.8 1A1I RADR GCAC 0.068 1A1J RADR GCGT (wild type) 0.035 1A1K RADR GACC 9.3 1A1L RDER (wild type) GCAC 5.6 1AAY RDER (wild type) GCGT (wild type) 2.7 This table reports on the names of the complexes, the specific sequences on Helix 1 that recognize DNA, DNA sequences, and the respective dissociation constants.

Publication Year: 2010

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 24914984 | PubMedCentral: PMC4051508 | DOI: 10.1107/S1399004714007603

As shown in Figs. 3 ▶ ( a ) and 3 ▶ ( b ), in the case of PDB fragments 1a1g and 1a1i (named after the PDB codes, where upper-case letters indicate the code for a test case and lower-c... se letters indicate the code for the source of a model) a TFZ score of about 6 turned into a solved structure after SHELXE with CC values above 22%, while for instance 2hgh with a TFZ score of 7 did not succeed.

Publication Year: 2014