Primary Citation PubMed: 11148030
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Selective prediction of interaction sites in protein structures with THEMATICS.
(2007) BMC Bioinformatics 8
PubMed: 17419878 | PubMedCentral: PMC1877815 | DOI: 10.1186/1471-2105-8-119
Protein Ligand Apo Holo PDB ID THEMATICS Result ATP:corrinoid adenosyltransferase ATP 1G5R K41 D127 E128 Y131 R161 1G5T K41 D127 E128 Y131 Intestinal Fatty Acid Binding Protein MYR 1IFB Y14 D34 Y70 R1... 6 Y117 R126 1ICM Y14 D34 R56 Y70 R106 Y117 HPV11 regulatory protein ALQ, 434 1R6K H29 H32 1R6N H29 H32 Proline 3-hydroxylase FE (II), sulfate 1E5R R97 H107 H135 H158 R168 H238 Y239 H244 1E5S R97 H107 H135 H158 H238 Y239 H244 Glyoxalase 1 Ni(II) 1FA8 H5 E56 Y72 H74 D115 D117 E122 1F9Z H5 E56 Y72 H74 D115 Y119 E122 β-Amylase maltose 1B90 Y14 Y44 D49 H89 Y164 E172 R174 Y310 E367 1B9Z Y14 Y44 D49 H89 Y164 E172 R174 Y178 K287 Y310 E367 GlcAT-P UDP, Mn(II) 1V82 E101 R104 D195 D196 D197 Y200 D254 1V83 E101 R104 D195 D196 D197 Y200 D254 Retinol-binding protein II retinal 1OPA Y19 Y60 C95 C121 1OPB Y19 C95 R104 C121 For each protein, the predicted binding cluster for the apo form is given in the top row and for the holo form in the second row.
Publication Year: 2007
Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites.
(2008) BMC Struct Biol 8
PubMed: 18954462 | PubMedCentral: PMC2626596 | DOI: 10.1186/1472-6807-8-45
To determine the extent that conformational variability exerts on similarity searching, we conducted retrieval experiments with query surfaces binding ATP in diverse conformations: cAMP- dependent kin... se (PDB: 1atp ) protein kinase CK2 from Z. mays (PDB: 1a6o )[ 53 ], ATP:corrinoid adenosyltransferase from S. typhimurium (PDB: 1g5t )[ 54 ], PurT-encoded glycinamide ribonucleotide transformylase from E. coli (PDB: 1kj8 )[ 55 ].
Binding surfaces representing different ATP conformational classes: cAMP- dependent kinase (PDB: 1atp , a), protein kinase CK2 from Z. Mays (PDB: 1a6o , b), ATP:corrinoid adenosyltransferase from S. typhimurium (PDB: 1g5t , c), PurT-encoded glycinamide ribonucleotide transformylase from E. coli (PDB: 1kj8 , d).
Publication Year: 2008
A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data.
(2011) BMC Bioinformatics 12
PubMed: 21356119 | PubMedCentral: PMC3058030 | DOI: 10.1186/1471-2105-12-64
Table 2 Manually Evaluated Nickel Protein Candidates Cluster number ORF Annotation Crystal structure homolog Metal In structure IPM prediction 2 PF0144 Aldolase-type TIM barrel Fe 2 PF1881 Alba archae... l DNA/RNA-binding protein 2Z7C 3 PF0038 Beta-lactamase-like glyoxalase II family member Zn 4 PF1916 Glycosyl transferase, family 2 4 PF1987 Conserved hypothetical protein 5 PF0056 Carbohydrate binding protein 1VJ2 Mn Mn 5 PF0138 Uncharacterized rubrerythrin domain protein 2FZF Fe 6 PF1664 Phosphoribosyl-AMP cyclohydrolase 1ZPS Cd Zn 6 PF2038 Adenosylcobalamin biosynthesis 1G5T Mg Co 7 PF1329 Hydrogenase II beta Fe 7 PF1331 Hydrogenase II delta Fe 7 PF1332 Hydrogenase II alpha Fe,Ni 8 PF0891 Hydrogenase I beta Fe 8 PF0894 Hydrogenase I alpha Fe,Ni 8 PF1500 PRC-barrel-like 8 PF1529 Pyroxidine biosynthesis protein 2YZR 12 PF1401 Peptidyl-prolyl cis-trans isomerase 13 PF0086 Alanyl-tRNA synthetase, class IIc 2E1B Zn 13 PF0615 Hydrogenase expression/formation protein A 3A43 Zn Ni 13 PF1272 LamB/YcsF 1V6T 13 PF1684 Acetylglutamate kinase 2EGX 13 PF1861 Lysyl aminopeptidase 2PE3 Zn Cluster number refers to hierarchical clustering with dynamic hybrid partitioning, see Figure 4 for explanation and supplementary tables 1-8 in Additional File 9 for complete cluster tables.
Publication Year: 2011
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