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PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models.

(2007) Acta Crystallogr D Biol Crystallogr 63

PubMed: 17452785 | PubMedCentral: PMC2483474 | DOI: 10.1107/S0907444907009791

Table 1 X-ray structural data used in this study PDB code d min (Å) R / R free Mean ADP (Å 2 ) Total chains Total residues Reference 1a0j 1.70 0.17/0.22 22.9 2 892 Kishan et al. (1997 ... #x025b6; ) 1a3n 1.80 0.17/0.22 16.2 4 572 J. Tame & B. Vallone, unpublished work 1bmb 1.80 0.19/0.22 22.5 2 106 Ettmayer et al. (1999 ▶ ) 1aof 2.00 0.16/0.20 25.8 2 1074 Williams et al. (1997 ▶ ) 1c2t 2.10 0.23/0.26 31.7 1 418 Greasley et al. (1999 ▶ ) 1uyi 2.20 0.18/0.22 28.3 1 209 Wright et al. (2004 ▶ ) 1rg5 2.50 0.16/0.18 52.9 3 824 Roszak et al. (2004 ▶ ) 1p4t 2.55 0.23/0.26 39.1 1 155 Vandeputte-Rutten et al. (2003 ▶ ) 1cqp 2.60 0.19/0.26 36.2 2 364 Kallen et al. (1999 ▶ ) 1c1z 2.88 0.24/0.24 55.3 1 326 Schwarzenbacher et al. (1999 ▶ ) Table 2 Characteristics of multiple rebuilt models       SD of models (precision, Å) R.m.s.d. among models (Å) R.m.s.d. between models and re-refined PDB entry (Å) PDB code d min (Å) ML estimate of coordinate error (Å) Main chain Side chain Main chain Side chain Main chain Side chain 1a0j 1.70 0.28 0.05 0.47 0.07 0.66 0.10 0.95 1a3n 1.80 0.35 0.03 0.38 0.04 0.54 0.06 0.68 1bmb 1.80 0.29 0.05 0.42 0.07 0.59 0.07 0.71 1aof 2.00 0.31 0.05 0.38 0.07 0.54 0.10 0.66 1c2t 2.10 0.41 0.13 0.56 0.18 0.79 0.19 0.98 1uyi 2.20 0.38 0.08 0.43 0.11 0.61 0.12 0.84 1rg5 2.50 0.44 0.14 0.44 0.20 0.62 0.18 0.62 1p4t 2.55 0.40 0.27 0.57 0.38 0.81 0.36 0.84 1cqp 2.60 0.41 0.12 0.53 0.17 0.75 0.18 0.93 1c1z 2.88 0.48 0.62 1.50 0.88 2.12 0.80 2.15 Table 3 Ensembles built using synthetic data     SD of models (precision, Å) R.m.s.d. from ‘mean perfect structure’ (Å) Resolution (Å) Mean free R factor Main chain Side chain Main chain Side chain 1.75 0.24 0.19 0.68 0.39 1.15 2.0 0.23 0.20 0.63 0.39 1.11 2.5 0.22 0.22 0.75 0.39 1.17 3.0 0.26 0.32 0.81 0.49 1.26 3.5 0.26 0.48 1.07 0.61 1.43 4.0 0.31 0.76 1.78 0.84 1.93 4.5 0.40 1.01 2.44 1.17 2.81 Table 4 Ensembles built using synthetic data at a resolution of 1.75 Å, beginning from different starting models       R.m.s.d. among models in ensemble (Å) R.m.s.d. between models and models in ensemble 1 (Å) Ensemble Main-chain r.m.s.d. of starting model from ensemble 1 (Å) Mean free R factor of structures in ensemble Main chain Side chain Main chain Side chain 1 0.00 0.24 0.19 0.72 — — 2 0.22 0.24 0.21 0.65 0.24 0.75 3 0.31 0.24 0.19 0.66 0.20 0.74 4 0.43 0.24 0.18 0.78 0.22 0.88 5 0.58 0.24 0.24 0.72 0.30 0.84 6 0.87 0.24 0.16 0.65 0.27 0.86 7 1.12 0.27 0.49 1.21 0.51 1.35

Publication Year: 2007


Automated ligand fitting by core-fragment fitting and extension into density.

(2006) Acta Crystallogr D Biol Crystallogr 62

PubMed: 16855309 | PubMedCentral: PMC2745883 | DOI: 10.1107/S0907444906017161

( b ) Fit at 2.2 Å of 8-(2,5-dimethoxybenzyl)-2-fluoro-9-pent-9 H -purin-6-ylamine (PDB entry 1uyi ; Wright et al. , 2004 ▶ ).

Publication Year: 2006


Identification of two novel HSP90 proteins in Babesia orientalis: molecular characterization, and computational analyses of their structure, function, antigenicity and inhibitor interaction.

(2014) Parasit Vectors 7

PubMed: 24970594 | PubMedCentral: PMC4089566 | DOI: 10.1186/1756-3305-7-293

Table 2 Interaction of Babesia orientalis HSP90-A and B isoforms with inhibitors using docking analysis Name Protein showing interaction Template ID PDB code Geldanamycin BoHSP90-A, BoHSP90-B Gmy1 2ex... Radamide BoHSP90-A, BoHSP90-B Rda1001 2gfd Redicicol BoHSP90-A, BoHSP90-B Rdc301 1u0z Dihydroxyphenylpyrazoles BoHSP90-A, BoHSP90-B 4BC401 1yc1 PU8(8-(2-chloro-3,4,5-trimethoxy-benzyl)-2-fluoro-9-pent-4-ylnyl-9 h-purin-6-ylamine) BoHSP90-B PU11224 1uyf PU11 (8-(2,5-dimethoxy-benzyl)-2-fluoro-9- pent-9 h-purin-6-ylamine) BoHSP90-A Puz1224 1uyi 1-(2-phenol)-2-naphthol BoHSP90-A, BoHSP90-B AB41226 2bz5 3,4-diaryl pyrazole resorcinol (CCT018159) BoHSP90-A, BoHSP90-B Ct51224 2bt0 4-amino derivative of 3,4-diaryl pyrazole (4-chloro-6-(4-piperazin-1-yl-1 h-pyrazol-3-yl)-benzene-1,2-diol) BoHSP90-B 4BH1224 2ccs The template IDs are the identification numbers of inhibitors in RCSB Protein Data Bank.

Publication Year: 2014