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PDB ID Mentions in PubMed Central

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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


Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations.

(2011) BMC Struct Biol 11

PubMed: 22017970 | PubMedCentral: PMC3207888 | DOI: 10.1186/1472-6807-11-44

The DNA, shown in green, is from PDB: 1C8C .

Average residence times of water molecules on the Sso7d surface derived from the MD simulations based on NMR (left) [PDB: 1JIC ] and X-ray (right) [PDB: 1C8C ] structures.

Molecular Dynamics 100 ns MD simulations were performed with explicit solvent using the lowest energy NMR structure of Sso7d [PDB: 1JIC ] [ 28 ] and the crystal structure of a Sso7d-DNA complex [PDB: 1C8C ] as the starting structures after removal of DNA and water molecules.

Molecular Dynamics simulation To minimize biased contributions from the Sso7d reference structures to the dynamics of the surface water molecules, two 100 ns MD simulations in explicit water were carried out using one crystal structure [PDB: 1C8C ] and one solution structure [PDB: 1JIC ].

In the Sso7d-GTGATCGC complex [PDB: 1C8C ], the backbone amide group of Lys28 and the N3 of G15 from the mismatched T-G base-pair are H-bond bridged via water 1128.

MDHS maps obtained from MD simulations carried out on the representative structures for solution NMR (left) [PDB: 1JIC ] and X-ray crystallography (right) [PDB: 1C8C ].

Superposition of three X-ray structures of Sso7d with a bound DNA duplex, yellow [PDB: 1BNZ ], orange [PDB: 1C8C ], red [PDB: 1BF4 ], and of two NMR structures for the free protein, cyan [PDB: 1JIC ], and blue [PDB: 1SSO ].

Ribbon representation of Sso7d [PDB: 1C8C ] showing the ePHOGSY signal intensity, the darker the blue, the stronger the signal; grey indicates regions where no signal was detected.

Methods Data set Three-dimensional structures, derived from NMR or X-ray experiments, of DNA-binding protein 7d from Sulfolobus solfataricus , Sso7d [UniProt:P39476] are available from the Protein Data Bank [ 29 ] both in the free form and in complexes with different DNA fragments [PDB: 1BF4 , PDB: 1BNZ , PDB: 1C8C , PDB: 1JIC , PDB: 1SSO ].

Distribution profiles of water residence times calculated from the MD simulations based on the X-ray (filled bars) [PDB: 1C8C ] and NMR (open bars) [PDB: 1JIC ] structures.

Publication Year: 2011


Rapid sampling of local minima in protein energy surface and effective reduction through a multi-objective filter.

(2013) Proteome Sci 11

PubMed: 24564970 | PubMedCentral: PMC3908317 | DOI: 10.1186/1477-5956-11-S1-S12

This difference in lRMSD is significant (0.5Å or greater) for proteins with native PDB ids 1fwp , 1ail , 1cc5 , 2ezk , 2h5nD for AMW and 1dtdB , 1c8cA , 1ail , 1aoy , 2ezk , 1hhp , 2hg6 , 2h5n... for Rosetta.

Rosetta Energy Function Native PDB Id Ω PF reduction Minimum lRMSD (Å) ( r = | Ω PF |/| Ω | ) Ω Ω TE ( r ) Ω PF Ω TE (5%) Ω TE (10%) Ω PC (5%) Ω PC (10%) 1 1dtdB 1% 6.7 10.8 9.1 10.6 10.2 10.2 8.6 2 1isuA 2% 6.5 8.9 8.6 8.9 8.6 8.0 7.5 3 1c8cA 2% 5.6 7.9 7.1 7.8 7.0 7.1 6.8 4 1sap 3% 6.1 7.4 7.1 7.4 6.8 6.8 6.6 5 1hz6A 3% 2.5 2.8 2.8 2.8 2.6 2.7 2.6 6 1wapA 1% 7.4 8.8 8.8 8.5 8.5 8.8 8.1 7 1fwp 3% 6.1 7.2 7.0 7.1 7.1 7.2 6.9 8 1ail > 1% 4.8 8.2 6.2 7.6 7.5 7.5 6.9 9 1aoy 2% 6.2 10.1 9.1 9.2 9.2 9.3 9.2 10 1cc5 1% 5.0 6.3 6.3 5.7 5.7 5.5 5.4 11 2ezk 1% 3.9 9.1 6.2 5.2 5.1 5.1 4.9 12 1hhp 3% 10.8 13.9 12.6 13.9 13.6 13.0 12.9 13 2hg6 2% 10.6 12.2 11.5 12.0 12.0 12.0 11.7 14 3gwl 1% 7.1 8.9 8.5 8.7 8.4 8.0 7.8 15 2h5nD 1% 8.9 13.0 10.4 12.3 12.1 12.2 11.4 The minimum lRMSD to the native structure retained by each of the proposed multi-objective ensemble reduction techniques is given for the Ω generated with the Rosetta energy function.

Native PDB id Size fold % α % β Lowest Energy (kcal/mol) Lowest lRMSD (Å) T = 0 T 0 T 1 T 2 T = 0 T 0 T 1 T 2 1 1dtdB 61 α/β 15 46 -128.2 -132.1 -131.6 -127.9 6.9 6.6 6.9 7.0 2 1isuA 62 α/β 15 19 -127.8 -130.3 -130.7 -130.2 6.3 6.0 6.4 6.0 3 1c8cA 64 α/β 22 48 -133.5 -134.8 -130.8 -129.6 6.5 6.6 7.4 7.3 4 1sap 66 α/β 30 44 -132.8 -132.3 -133.6 -127.3 6.5 6.0 6.8 6.9 5 1hz6A 67 α/β 31 42 -143.5 -144.7 -142.1 -138.9 5.7 5.9 6.0 6.0 6 1wapA 68 β 0 62 -118.4 -127.2 -133.9 -127.9 7.4 7.6 7.4 7.5 7 1fwp 69 α/β 30 26 -152.8 -152.0 -143.5 -143.2 6.3 6.7 6.5 6.1 8 1ail 70 α 84 0 -170.6 -171.0 -167.3 -168.4 3.2 3.2 3.4 3.3 9 1aoy 78 α/β 41 10 -183.9 -181.2 -180.8 -184.1 5.7 6.4 6.0 6.4 10 1cc5 83 α 47 4 -170.9 -171.5 -179.1 -173.8 5.8 5.7 5.8 5.8 11 2ezk 93 α 68 0 -217.3 -218.6 -224.4 -216.0 4.3 4.6 4.2 4.4 12 1hhp 99 β 7 48 -168.7 -175.4 -179.0 -175.9 10.4 10.4 10.0 10.5 13 2hg6 106 α/β 34 21 -233.6 -236.8 -239.5 -235.1 8.8 9.0 8.8 9.2 14 3gwl 106 α 70 0 -264.6 -270.4 -273.9 -267.3 4.9 4.9 4.4 5.2 15 2h5nD 123 α 71 2 -307.8 -313.0 -316.5 -313.2 7.5 7.9 7.4 8.1 Columns 2-4 show the native PDB id, size and fold topology for each of the 15 target protein systems.

AMW Energy Function Native PDB Id Ω PF reduction Minimum lRMSD (Å) ( r = | Ω PF |/| Ω | ) Ω Ω TE ( r ) Ω PF Ω TE (5%) Ω TE (10%) Ω PC (5%) Ω PC (10%) 1 1dtdB 4% 7.2 7.9 7.7 7.9 7.7 7.7 7.7 2 1isuA 7% 6.0 6.2 6.5 6.4 6.2 6.2 6.2 3 1c8cA 4% 7.4 7.5 7.5 7.5 7.5 7.5 7.5 4 1sap 2% 6.5 7.6 7.5 7.4 7.2 7.4 7.2 5 1hz6A 2% 5.9 6.7 6.3 6.7 6.7 6.7 6.6 6 1wapA 2% 7.7 8.7 8.7 8.7 8.7 8.7 8.7 7 1fwp 7% 6.4 8.1 7.3 8.1 8.1 8.1 8.1 8 1ail 2% 3.4 6.8 5.9 5.8 4.2 4.7 4.4 9 1aoy 6% 5.7 6.9 6.6 6.9 6.5 6.8 6.5 10 1cc5 7% 5.6 8.6 7.0 8.7 8.6 8.6 8.1 11 2ezk 3% 4.4 8.0 7.3 7.7 7.1 7.2 7.1 12 1hhp 1% 10.7 12.0 12.0 11.6 11.6 11.6 10.8 13 2hg6 6% 8.6 10.8 10.5 11.6 10.8 10.9 10.8 14 3gwl 5% 4.2 4.7 5.2 4.7 4.7 4.7 4.7 15 2h5nD 7% 7.9 10.7 10.0 10.8 10.4 10.4 10.4 The minimum lRMSD to the native structure retained by each of the proposed multi-objective ensemble reduction techniques is given for the Ω generated with the AMW energy function.

Publication Year: 2013