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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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Super-resolution biomolecular crystallography with low-resolution data.

(2010) Nature 464

PubMed: 20376006 | PubMedCentral: PMC2859093 | DOI: 10.1038/nature08892

For the unligated SIV gp120 structure 18 (PDB 2bf1) we restricted the DEN network to the main chain and Cβ-atoms of the reference model (HIV gp120-antibody complex at 2.0 Å resolution ... 9 , PDB 2nxz) and to regions of the structure considered reliable predictors of SIV gp120 structure (at least 35.8 % local sequence identity, Supplementary Table 2 ).

Publication Year: 2010


Novel ligands for a purine riboswitch discovered by RNA-ligand docking.

(2011) Chem Biol 18

PubMed: 21439477 | PubMedCentral: PMC3119931 | DOI: 10.1016/j.chembiol.2010.12.020

Table 2 Crystallographic Data and Refinement Statistics of GRA-Ligand Complexes Details of Data Collection Ligand Complex 14 24 26 27 PDB Code 2xo1 2nxw 2nxz 2xo0 Space Group C2 C2 C2 C2 Unit Cell Dim... nsions (Å) a = 132.762 a = 135.895 a = 132.165 a = 130.923 b = 35.180 b = 35.380 b = 35.068 b = 34.940 c = 41.763 c = 42.197 c = 41.778 c = 42.074 β = 90.51 β = 92.20 β = 92.06 β = 92.11 Resolution Range (Å) 20–1.6 (1.66–1.6) 67.88–1.5 (1.55–1.5) 60.08–1.6 (1.66–1.6) 65.5–1.7 (1.76–1.7) Observations 72,587 80,100 93,460 62,872 Unique Observations 25,098 30,250 25,334 21,077 Completeness (%) 96.5 (91.0) 93.1 (97.9) 98.5 (98.1) 96.8 (93.5) <I/σ(I) > 20.6 (2.7) 18.0 (2.3) 30.2 (2.9) 26.8 (3.1) R merge a (%) 5.3 (25.8) 6.2 (38.5) 4.4 (39.8) 5.2 (39.1) Refinement Statistics Resolution Range (Å) 20–1.6 67.88–1.5 66.08–1.6 65.51–1.7 R-factor b % (R work /R free ) 19.5/21.1 21.4/24.4 19.8/23.4 21.6/27.1 Number of atoms c 1364/11/226/56 1366/10/329/54 1382/9/216/52 1363/16/151/55 Mean B -factor d (Å 2 ) 22.7/18.3/29.0/25.8 21.7/22.1/29.0/23.8 24.9/22.7/29.2/27.9 29.6/26.3/30.2/32.7 RMS bond length deviation (Å) 0.008 0.009 0.009 0.013 RMS bond angle deviation (°) 1.508 1.683 1.546 1.973 Values in brackets are for the highest resolution shell.

49 2005 3367 3372 16048949 Accession Numbers Coordinates have been deposited in the PDB with accession codes 2xo1 , 2nxw , 2nxz , and 2xo0 .

Publication Year: 2011


CD4 binding determinant mimicry for HIV vaccine design.

(2012) Front Immunol 3

PubMed: 23251137 | PubMedCentral: PMC3523313 | DOI: 10.3389/fimmu.2012.00383

, CD4 liganded 1GC1, 1G9M, 1G9N, 1RZJ, 1RZK, 3JWD, 3JWO, 2NXY, 2NXZ, 2NY5, 2B4C, 2QAD; unliganded 2BF1, 3TGQ, 3TGR, 3TGT, 3TIH; CD4BD OD antibody liganded 3NGB, 3SE8, 3SE9, 3U7Y, 2NY7, 3HI1, 3IDX; low... molecular-weight CD4 mimetic liganded 1YYL, 1YYM, 2I5Y, 2I60, 3TGS).

Publication Year: 2012