Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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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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The JCSG MR pipeline: optimized alignments, multiple models and parallel searches.

(2008) Acta Crystallogr D Biol Crystallogr 64

PubMed: 18094477 | PubMedCentral: PMC2394805 | DOI: 10.1107/S0907444907050111

165 P 2 1 2 1 2 2 1.50 18.7 1g76 14     X 1vl7 tm1459, carbohydrate-binding protein, T. maritima 114 P 32 2 1.75 11.8 1lr5 18     X 1o5u tm1287, oxalate decarboxylase, ... . maritima 121 C 2 2 1.70 8.9 1vj2 18   X X 1o4t 15079298, glia maturation factor-γ, Mus musculus 142 P 1 1 1.35 15.7 1ahq 19 X X X 1vkk tm0603, 30s ribosomal protein s6, T. maritima 128 P 4 1 2 1 2 1 1.70 15.0 1lou 19     X 1vmb 17391249, haloacid dehalogenase-like hydrolase, M. musculus 248 P 6 1 22 1 1.90 12.0 1x42 19     X 2gfh tm1394, heat-shock protein 33, T. maritima 290 P 2 1 2 1 2 1 2 2.00 8.6 1i7f 20     X 1vq0 18044849, bifunctional coenzyme A synthase, M. musculus 269 C 2 1 1.70 15.0 1n3b 22     X 2f6r tm0820, NADH-dependent butanol dehydrogenase, T. maritima 395 P 2 1 2 1.78 10.0 1o2d 24     X 1vlj tm0332, orotidine 5′-phosphate decarboxylase, T. maritima 201 C 2 1 1.90 9.2 1eix 24     X 1vqt 10175646, BH3024 protein, Bacillus halodurans 126 P 4 1 2 1 2 1 2.40 6.5 1kgs 25 X X X 2b4a NP_394403, GMP synthase, T. acidophilum 212 P 2 1 2 1 2 4 2.45 4.4 1gdl 25     X 2a9v tm0262, DNA polymerase III, β subunit, T. maritima 366 P 4 2 2 1 2 1 2.70 4.8 1jqj 26     X 1vpk tm1419, myo -inositol-1-phosphate synthase, T. maritima 382 I 222 1 1.58 22.5 1gr0 26   X X 1vjp YP_290749.1, NADH dehydrogenase subunit C, T. fusca YX 252 P 4 3 2 1 2 1 2.60 8.6 2fug 27     X   tm1088A, hypothetical protein, T. maritima 143 P 2 1 1.50 20.3 1lss 27 X X X 2g1u tm0748, SAM-dependent O -methyltransferase, T. maritima 265 I 222 1 1.70 16.7 1i9g 28 X X X 1o54 tm0544, ABC transporter ATP-binding protein, T. maritima 244 P 3 1 2 1 1 2.10 10.6 1ji0 29     X 1vpl tm1128, ferritin, T. maritima 182 H 32 8 2.35 8.1 1eum 30 X X X 1vlg tm0295, transaldolase, T. maritima 218 P 2 1 20 2.40 5.1 1l6w 30     X 1vpx tm0343, DAHP synthase, T. maritima 338 P 2 1 2 1 2 1 3 1.90 8.5 1fwn 31 X X X 1vr6 tm1385, glucose-6-phosphate isomerase, T. maritima 448 I 2 1 2 1 2 1 3 2.90 6.8 1b0z 31   X X   tm1645, quinolinate phosphoribosyltransferase, T. maritima 273 I 222 2 2.80 6.9 1qpn 31     X 1o4u tm0066, 2-dehydro-3-deoxyphosphogluconate aldolase, T. maritima 205 C 222 1 3 2.30 6.8 1eua 31   X X 1vlw tm1393, MEP cytidylyltransferase, T. maritima 222 P 6 1 2 2.60 6.7 1vgz 31     X 1vpa tm1244, phosphoribosylformylglycinamidine synthase, T. maritima 82 I 4 1 22 4 2.50 7.0 1t4a 32     X 1vq3 tm0166, dihydrofolate synthase, T. maritima 430 P 6 1 22 1 2.75 8.9 1fgs 32 X X X 1o5z tm0919, hydroperoxide-resistance protein OsmC, T. maritima 138 P 2 1 4 1.80 12.9 1ml8 33     X 1vla tm1698, aspartate aminotransferase, T. maritima 397 P 2 1 6 2.50 4.1 1xi9 29 X X X 2gb3 tm0604, single-stranded DNA-binding protein, T. maritima 141 F 222 1 2.40 10.0 1qvc 34   X X 1z9f tm1169, 3-oxoacyl-(acyl carrier protein) reductase, T. maritima 237 P 2 1 2 1 2 1 4 2.50 4.3 1i01 34   X X 1o5i 17130499, anthranilate phosphoribosyltransferase 2, Nostoc sp.

Publication Year: 2008


Structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Rickettsia prowazekii at 2.25 resolution.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67

PubMed: 21904060 | PubMedCentral: PMC3169412 | DOI: 10.1107/S1744309111030673

In this figure, the monomers of FabG from R. prowazekii (PDB entry 3f9i ; purple helices, yellow strands), from E. coli (PDB entry 1i01 ; magenta), from M. tuberculosis (PDB entry 1uzm ; light blue) a... d the NADP + -bound structure from V. cholerae (PDB entry 3rsk , pink) are superimposed.

Comparison with other bacterial 3-ketoacyl-(ACP) reductases The R. prowazekii FabG shows 1.33 Å r.m.s.d. with the E. coli structure (PBD entry 1i01 ; Price et al. , 2001 ▶ ) over 205 residues, 1.26 Å r.m.s.d. with the M. tuberculosis structure (PDB entry 1uzm ; Cohen-Gonsaud et al. , 2002 ▶ ) over 201 residues and 1.22 Å r.m.s.d. with the NADP + -bound Vibrio cholerae structure (PDB entry 3rsh ; J. Hou, M. Chruszcz, D. Cooper, M. Grabowski, H. Zheng, T. Osinski, I. Shumilin, W. Anderson & W. Minor, unpublished work) over 208 residues, as shown in Fig. 3 ▶ , whereas the r.m.s.d. with Sus scrofa mammalian FAS (PDB entry 2vz8 ; Maier et al. , 2008 ▶ ), used here as a homologue for the unsolved human FAS structure, is 2.5 Å over 80%.

From top to bottom: E. coli , 1i01 (Price et al. , 2001 ▶ ); M. tuberculosis , 1uzm (Cohen-Gonsaud et al. , 2002 ▶ ); Pseudomonas aeruginosa , 2b4q (Miller et al. , 2006 ▶ ); Aquifex aeolicus , 2pnf (Q. Mao, R. Huether, W. L. Duax & T. C. Umland, unpublished work); R. prowazekii , 3f9i (this work); Burkholderia pseudomallei , 3ftp (Seattle Structural Genomics Center for Infectious Disease, unpublished work); Bartonella henselae , 3grp (B. L. Staker, unpublished work); Brucella melitensis , 3n74 (Seattle Structural Genomics Center for Infectious Disease, unpublished work).

Publication Year: 2011


BdcA, a protein important for Escherichia coli biofilm dispersal, is a short-chain dehydrogenase/reductase that binds specifically to NADPH.

(2014) PLoS One 9

PubMed: 25244619 | PubMedCentral: PMC4171110 | DOI: 10.1371/journal.pone.0105751

B ) Superposition of the residues that constitute the catalytic triad in BcdA (dark pink) and E. coli apo-FabG (gray, PDB:1I01; catalytically incompetent) and E. coli FabG bound to NADP+ (cyan, PDB:1Q... B; catalytically competent).

In E. coli FabG (PDB 1I01), these loops are disordered in the absence of cofactor, but become ordered when bound to NADP+ (PDB 1Q7B, Table 2 ) and orient the catalytic residues in the optimal positions for catalysis ( Figure 2B ) [32] .

Publication Year: 2014