Primary Citation PubMed: 1857417
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
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.
Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation.
(2007) Nucleic Acids Res 35
PubMed: 17284460 | PubMedCentral: PMC1865053 | DOI: 10.1093/nar/gkl1164
Residues interacting in E. coli binary and ternary complexes (1O0B, 1GTR) with ATP/AMP, Gln/5′O[ N -( l -Gln)sulfamoyl] adenosine and tRNA are indicated by A (a), Q (q) or R (r), respectively ... lower case letters are for main-chain interactions, upper case letters for side-chain contacts) and hQ stands for side-chain interactions with glutamine mediated by H 2 O molecules.
Publication Year: 2007
Computer-based screening of functional conformers of proteins.
(2008) PLoS Comput Biol 4
PubMed: 18463705 | PubMedCentral: PMC2265533 | DOI: 10.1371/journal.pcbi.1000009
PDB Code Protein Name Ligand Name SCOP Classification 1BJY Tetracyclin repressor Tetracycline All alpha 1DQY Antigen85c (mycolyltransferase) Diethyl phosphate inhibitor Alpha/beta 1CRX CRE recombinase... DNA All alpha 1EX7 Guanylate kinase Guanosine 5-monophosphate All beta 1QUK Phosphate-binding protein Phosphate Alpha/beta 1GTR Glutaminyl-tRNA synthase ATP Alpha/beta 2DRI Ribose-binding protein Ribose Alpha/beta 1SSP Uracyl-DNA glycosylase Uracyl-DNA Alpha/beta 1CIP Guanine nucleotide-bindign protein Phosphoaminophosphonic acid-guanylate ester Alpha/beta 3PJR Helicase DNA Alpha/beta 1B0O Beta-Lactoglobulin Palmitate All beta 6TIM TriosePhosphate Isomerase 3-Phosphoglycerol Alpha/beta 1F8A Peptidyl-prolyl cis-trans isomerase Phosphoserine-proline peptide Alpha + beta 1DVJ Orotinide monophosphate dehydrogenase 6-AZA Uridine MonoPhosphate Alpha/beta 1FTM Glutamate receptor AMPA Alpha/beta 3MBP Maltose-binding protein Maltotriose Alpha/beta 1QAI Reverse transcriptase Nucleic acid Multidomain protein (alpha and beta) 2RKM Oligopeptide binding protein Lys-Lys peptide Alpha/beta 1I7D DNA toposiomerase II 8-bases single-stranded DNA Multidomain protein (alpha and beta) 1PFK Phosphofructokinase Fructose diphosphate Alpha/beta The proteins solved in complex with a ligand in the MolMov set are listed with their ligands.
The PDB codes in the MolMov subset I include: 1bjy, 1b0o, 1dqy, 6tim, 1f8a, 1dvj, 1crx, 1ex7, 1ftm, 3mbp, 1qai, 2rkm, 1quk, 1gtr, 2dri, 1ssp, 1i7d, 1cip, 1pfk and 3pjr.
Publication Year: 2008
Multimerization and H3K9me3 binding are required for CDYL1b heterochromatin association.
(2009) J Biol Chem 284
PubMed: 19808672 | PubMedCentral: PMC2787366 | DOI: 10.1074/jbc.M109.052332
Despite these amino acid exchanges, structural superposition of the CDYL1 ECH-like domain (PDB 1gtr ) and the rat peroxisomal ECH (PDB 1dub ) show that the overall trimeric-fold of these proteins rema... ns unchanged ( Fig. 5 B ).
B , tertiary and quaternary structures of human CDYL1 (1gtr, red ) and rat ECHP (1dub, blue ) as determined by x-ray crystallography are shown.
Publication Year: 2009
Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome.
(2010) Nucleic Acids Res 38
PubMed: 20139416 | PubMedCentral: PMC2879513 | DOI: 10.1093/nar/gkq031
( B ) The GU-like juxtaposition observed in base pairs A 105 –C 112 and A 113 –C 104 (pdb entry code 402d) ( 27 ), A 11 –C 22 and A 27 –C 6 (pdb entry code 405d) ( 28 )... A 5 –C 24 and A 23 –C 6 (pdb entry code 1d4r) ( 29 ), A 139 –C 158 and A 157 –C 140 (pdb entry code 1jid) ( 30 ), A 26 –C 44 (pdb entry codes 1o0b, 1qtq, 1gtr, 1qru) ( 31–34 ), A 1500 –C 1402 (pdb entry code 1j5e) ( 35 ), A 192 –C 178 (pdb entry code 1u9s) ( 36 ) and A 44 –C 26 (pdb entry code 1y27) ( 37 ).
Publication Year: 2010
M-ORBIS: mapping of molecular binding sites and surfaces.
(2011) Nucleic Acids Res 39
PubMed: 20813758 | PubMedCentral: PMC3017595 | DOI: 10.1093/nar/gkq736
In the case of the DNA dataset, six structures (1asy; 1gtr; 1zdi; 1urn; 1ttt; 1ser) were identified as participating in protein–RNA interactions rather than protein–DNA interactions bu... the consultation of the structures proves M-ORBIS to be right, where the nucleic acids were mainly tRNA (1asy; 1gtr; 1zdi; 1ser).
Publication Year: 2011
Searching the protein structure database for ligand-binding site similarities using CPASS v.2.
(2011) BMC Res Notes 4
PubMed: 21269480 | PubMedCentral: PMC3057182 | DOI: 10.1186/1756-0500-4-17
Receiver operating characteristics (ROC) curves for two representative CPASS calculations of the proteins, aspartate transaminase (PDB: 1yaa, E.C. 22.214.171.124) and glutamine-tRNA ligase (PDB: 1gtr, E.C. 6... 1.1.18) are shown in figure 7A,B .
Evaluation of CPASS performance Six different proteins were evaluated using CPASS: glycine hydroxymethyltransferase (PDB: 1 kkp, E.C. 126.96.36.199); aspartate transaminase (PDB: 1yaa, E.C. 188.8.131.52); pyruvate kinase (PDB: 3hqo, E.C. 184.108.40.206); phosphoenolpyruvate carboxykinase (PDB: 1xkv, E.C. 220.127.116.11); glutamine-tRNA ligase (PDB: 1gtr, E.C. 18.104.22.168); and biotin carboxylase (PDB: 1dv2, E.C. 22.214.171.124).
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking.
(2011) BMC Bioinformatics 12
PubMed: 21851628 | PubMedCentral: PMC3179970 | DOI: 10.1186/1471-2105-12-348
There are 72 protein-RNA complexes in the training set taken from crystal structures of protein-RNA complexes downloaded from the Protein Data Bank (PDB codes: 1a1v , 1a34 , 1b2m , 1c0a , 1d9d , 1dfu ... 1di2 , 1bu1 , 1ec6 , 1f7u , 1feu , 1ffy , 1fxl , 1gtf , 1gtr , 1hq1 , 1j1u , 1jbs , 1jid , 1jj2 - 50S ribosome structure, 1k8w , 1knz , 1lng , 1m8w , 1mji , 1msw , 1n35 , 1n78 , 1ooa , 1qln , 1r3e , 1r9f , 1rc7 , 1sds , 1tfw , 1u0b , 1urn , 1uvj , 1wsu , 1yvp , 1zbi , 1a8v , 2bgg , 2bh2 ) [ 25 ].
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.