Citations in PubMed

Primary Citation PubMed: 8654383 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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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 [53] .

Publication Year: 2013