Primary Citation PubMed: 2329585
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ResBoost: characterizing and predicting catalytic residues in enzymes.
(2009) BMC Bioinformatics 10
PubMed: 19558703 | PubMedCentral: PMC2713229 | DOI: 10.1186/1471-2105-10-197
In summary, the PDB ID's for the proteins (and their included chain) are: 1qdl-A , 1b8g-B , 1fps , 1mfp-A , 1arz-A , 1d3g-A , 1qb4-A , 1kas , 1a7u-A , 1dii-A , 1grc-A , 1uag , 1zio , 1ay4-A , 1bou-B ,... 1b73-A , 1q91-A , 1daa-A , 1cd5-A , 1aq0-A , 1fdy-A , 1ecx-A , 1qba , 1kc7-A , 1pja-A , 1hdh-A , 1geq-B , 1exp , 1aql-A , 1b66-A , 1qum-A , 1d7r-A , 1qd6-C , 1cz1-A , 5enl , 1ah7 , 1pmi , 1og1-A , 1tph-1 , 1ey2-A , 1ahj-A , 1pnl-B , 1ir3-A , 1oe8-B , 1d0s-A , 1gim , 1std , 1a0i , 1aop , 1qcn-B , 1get-B , 1uqt-A , 1m6k-A , 1trk-A , 1sme-A , 2ts1 , 1ps9-A , 1ecl , 1ef0-A , 1aj0 , 2dhn , 1akd , 7odc-A , 135l , 1fcb-A , 1cbg , 1f8m-A , 1aj8-A , 1cel-A , 1l8t-A , 1jms-A , 1mrq-A , 1qh9-A , 1mlv-B , 1mhl-D , 1f75-A , 1d6o-A , 1b57-A , 1chd , 1bwz-A , 1nln-A , 1nba-A , 1cmx-A , 1xik-B , 1lnh , 1opm-A , 1lxa , 1a50-B , 1yve-L , 1d2r-A , 1bt1-A , 1ab8-A , 1dbt-A , 1amo-A , 1p4r-A , 1eyp-A , 1do8-A , 1oyg-A , 1rbn , and 1qmh-B .
Publication Year: 2009
Composite structural motifs of binding sites for delineating biological functions of proteins.
(2012) PLoS One 7
PubMed: 22347478 | PubMedCentral: PMC3275580 | DOI: 10.1371/journal.pone.0031437
Cytochrome and glycolate oxidase (GOX) Mitochondrial cytochrome , also known as L-lactate dehydrogenase, from Saccharomyces cerevisiae (PDB 1FCB  , chain A, EC 220.127.116.11) and glycolate oxidase (GOX)... from spinach (PDB 1AL7  , chain A, EC 18.104.22.168) share the TIM-barrel fold with 40% sequence identity, and have the same elementary motif for flavin mononucleotide (FMN) ( Fig. 4D ).
Publication Year: 2012
Rationally re-designed mutation of NAD-independent L-lactate dehydrogenase: high optical resolution of racemic mandelic acid by the engineered Escherichia coli.
(2012) Microb Cell Fact 11
PubMed: 23176608 | PubMedCentral: PMC3526519 | DOI: 10.1186/1475-2859-11-151
The X-ray crystal structure of flavocytochrome b 2 has been resolved (PDB ID code 1FCB), and the active site for 2-α-hydroxyacid dehydrogenation has been identified [ 23 ].
The figure is generated according to the molecular structure of flavocytochrome b 2 at 2.4 Å resolution (PDB code 1FCB) [ 23 ] with PyMOL (The PyMOL Molecular Graphics System, Version 0.99rc6, Schrödinger, LLC).
A rule-based algorithm for automatic bond type perception.
(2012) J Cheminform 4
PubMed: 23113939 | PubMedCentral: PMC3557220 | DOI: 10.1186/1758-2946-4-26
The first data set collected by Ricketts et al. [ 15 ] has 17 ligands extracted from the PDB files (PDB entries are 1cla, 1fcb, 1fx1, 1gox, 2aat, 2dhf, 2gbp, 2trm, 3cpp, 3ptb, 4dfr, 4xia, 5xia, 7dfr, ... atc, and 8rsa), and it has been extensively used for testing the algorithms of bond assignment.
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