Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 2

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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The NMR structure of the murine DLC2 SAM domain reveals a variant fold that is similar to a four-helix bundle.

(2007) BMC Struct Biol 7

PubMed: 17519008 | PubMedCentral: PMC1899508 | DOI: 10.1186/1472-6807-7-34

Table 2 Interhelical angles of selected four-helix bundles and SAM domains a PDB b Name Helix Pair c H1-H2 H2-H3 H3-H4 H4-H5 H5-H1 H2-H4 2JMT DLC2 -163 NA NA 156 147 -150 1P68 S-824 177 NA NA -156 -17... -159 1FLX FELIX -164 NA NA -165 -166 -160 1SVO Mae 138 75 109 141 124 NA 1SV4 Yan 138 95 108 138 124 NA 1F0M EphB2 153 95 108 138 124 NA 1DXS p73 154 96 112 129 124 NA 1PK3 Scm 162 102 112 135 75 NA 1KW4 Ph 161 112 -87 155 118 NA 1B0X EphA4 149 97 -113 127 118 NA 1OW5 Ste11 145 100 -114 112 132 NA 1Z1V Ste50 158 101 -116 121 115 NA Average d 151 97 13 132 117 SD e 9 10 115 12 17 a Calculated with the program INTERHLX b Protein Data Bank accession number c To facilitate a comparison with five-helix SAM domains, the helix order of 2JMT, 1FLX and 1P68 is defined as H1-H2-H4-H5 d Average angles are calculated only for the five-helix SAM domains e Standard deviations are calculated only for the five-helix SAM domains A dynamics study was performed to supplement the DLC2-SAM domain structure determination.

Publication Year: 2007


Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures.

(2009) BMC Bioinformatics 10 Suppl 1

PubMed: 19208142 | PubMedCentral: PMC2648730 | DOI: 10.1186/1471-2105-10-S1-S40

PDB N AA Pct N N α N b N m N eff Pct eff 1BW6 56 58.93% 4 0 384 9 2.34% 1DV5 80 46.25% 3 0 48 2 4.17% 1HDJ 77 48.05% 4 0 384 1 0.26% 1K6U 58 44.83% 2 2 64 13 20.31% 1RZL 91 56.04% 4 0 384 4 1.... 4% 1YRI 35 71.43% 3 0 48 5 10.42% 1FK5 93 53.76% 4 0 384 3 0.78% 1G6X 58 44.83% 2 2 64 4 6.25% 1I2T 61 88.52% 4 0 384 2 0.52% 1WPA 107 85.98% 3 0 48 4 8.33% 2NLS 36 47.22% 1 3 96 27 28.12% 1B0X 72 61.11% 5 0 3840 167 4.35% 1KDX 81 66.67% 5 0 3840 6 0.16% 1NFO 131 83.97% 5 0 3840 2 0.05% 1NKL 78 65.38% 5 0 3840 2 0.05% 1UNK 87 55.17% 5 0 3840 7 0.18% 1A0B 117 78.63% 6 0 46080 9 0.02% 1EIJ 72 68.06% 4 2 3072 27 0.88% 1F1F 88 64.77% 6 0 46080 39 0.08% 1FIO 190 88.95% 6 0 46080 2 0.00% 1ZVA 75 88.00% 2 0 8 0 0.00% 1TQG 105 86.67% 4 0 384 0 0.00% 2CC6 64 71.88% 1 3 96 1 1.04% 2END 137 42.34% 3 0 48 5 10.42% 2G7O 68 80.88% 4 0 384 5 1.30% 1NKD 59 86.44% 2 0 8 0 0.00% 2MHR 118 60.17% 5 0 3840 13 0.34% 1NGR 85 56.47% 6 0 46080 102 0.22% 1USM 77 61.04% 2 4 3072 28 0.91% 2OVG 58 67.24% 3 3 2304 19 0.82% N AA : number of amino acids Pct N : the percentage of amino acids in the secondary structures (helices and strands); N α : the number of alpha helix; N b : gthe number of beta strands; N m : the gnumber of secondary structure mutations, the cross mutation between a helix and a strand is ignored; N eff : the gnumber of the mutated topologies with lower effective contact energy than that of the native; Pct eff : the percentage of the mutated topologies with lower effective contact energy than that of the native by multi-well function; We tested the approach in stage 2 with four small α -proteins.

Publication Year: 2009