Primary Citation PubMed: 1857417
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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. 184.108.40.206) 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. 220.127.116.11); aspartate transaminase (PDB: 1yaa, E.C. 18.104.22.168); pyruvate kinase (PDB: 3hqo, E.C. 22.214.171.124); phosphoenolpyruvate carboxykinase (PDB: 1xkv, E.C. 126.96.36.199); glutamine-tRNA ligase (PDB: 1gtr, E.C. 188.8.131.52); and biotin carboxylase (PDB: 1dv2, E.C. 184.108.40.206).
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 ].
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