Primary Citation PubMed: 8654383
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Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.
(2006) BMC Bioinformatics 7
PubMed: 16790052 | PubMedCentral: PMC1534064 | DOI: 10.1186/1471-2105-7-312
The 79 proteins (identified by the PDB code) were: 1a26, 1a4i, 1a4s, 1ab8, 1ae7, 1afw, 1ah7, 1akm, 1aop, 1apx, 1apy, 1aq2, 1aw8, lb3r, lb57, lb93, 1bo1, 1brm, 1bs4, 1btl, 1bzy, 1cd5, 1chd, 1ctt, 1d4a,... 1daa, 1dae, 1db3, 1dbt, 1dco, 1diz, 1dj0, 1dnk, 1dnp, 1dqs, 1dzr, 1e2a, 1ef8, 1eyi, 1fua, 1gim, 1gpm, 1gpr, 1grc, 1hxq, 1iph, 1jdw, 1kas, 1kra, 1lba, 11xa, 1mbb, 1mek, 1mla, 1moq, 1mpy, 1nba, 1nsp, 1pfk, 1pjb, 1pnl, 1pud, 1qfe, 1smn, 1uae, 1ula, 1uok, 1uox, 1wgi, 1xva, 2acy, 2alr, 2bbk, 2cpo, 2hgs, 2jcw, 2pfl, 2plc, 3eca.
Publication Year: 2006
How accurate and statistically robust are catalytic site predictions based on closeness centrality?
(2007) BMC Bioinformatics 8
PubMed: 17498304 | PubMedCentral: PMC1876251 | DOI: 10.1186/1471-2105-8-153
Table 3 Dataset used in comparison of ligated and unligated pairs Enzyme 1 Ligated vs. unligated 2 Protein length SCOP class Correl 3 RMSD (Å) 4 4-oxalocrotonate tautomerase (1BJP, 4OTB) 1, 2,... 0 59 α + β 0.985 0.4 Ribonuclease A (1RBN, 1RSM) 0, 2, 2 124 α + β 0.984 0.6 Xylanase II (1BVV, 1XNB) 1, 1, 0 185 β 0.997 0.2 Trpysin (1A0J, 1UTK) 1, 2, 0 245 β 0.983 1.1 Aminopeptidase (1IGB, 1AMP) 1, 0, 0 291 α/β 0.992 0.6 Phospholipase C (1AOD, 2PLC) 3, 0, 2 294 α/β 0.992 0.2 Deacetoxycephalosporin C synthase (1W2N, 1W28) 0, 1, 0 298 β 0.980 0.5 Chorismate mutase (3CSM, 2CSM) 2, 2, 0 300 α 0.955 1.9 Alginate lyase A1-III (1HV6, 1QAZ) 2, 0, 1 354 α 0.995 0.1 tRNA-guanine transglycosylase (1R5Y, 1PUD) 1, 0, 0 382 α/β 0.814 0.5 Nitric oxide synthase oxygenase (1M9R, 3NOS) 2, 2, 0 480 α + β 0.992 0.2 Luciferase (1BA3, 1LCI) 3, 1, 0 544 Multi.
Publication Year: 2007
Investigation of specificity determinants in bacterial tRNA-guanine transglycosylase reveals queuine, the substrate of its eucaryotic counterpart, as inhibitor.
(2013) PLoS One 8
PubMed: 23704982 | PubMedCentral: PMC3660597 | DOI: 10.1371/journal.pone.0064240
Coordinates of the apo-Tgt crystal structure (PDB-code: 1pud in case of the structures 3bl3 , 3bld , 3blo ) or rather coordinates of Tgt in complex with 2-[(thiophen-2-ylmethyl)amino]-1,7-dihydro-8H-i... idazo[4,5-g]quinazolin-8-one (PDB-code: 3gev in case of structures 4dg0 , 4e2v , 4hvx , 4h7z , 4h6e , 4hsh , 4hqv , 4gcx and “WT”-Tgt·queuine) were slightly modified (deletion of water and ligand as well as coordinates at the sites of mutation) before applying for initial rigid-body refinement of the protein molecule followed by repeated cycles of conjugate gradient energy minimisation, simulated annealing and B -factor refinement using the CNS program package  .
Publication Year: 2013
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