Citations in PubMed

Primary Citation PubMed: 16421930 Citations in PubMed

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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Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.

(2010) Biol Direct 5

PubMed: 20433725 | PubMedCentral: PMC2876114 | DOI: 10.1186/1745-6150-5-31

Table 2 Enzymes with multiple structurally distinct, non-homologous isoforms Enzyme name (EC) Example (SwissProt) Structure (PDB) Fold names in SCOP (abbreviated) Acid phosphatase (EC 3.1.3.2) PPA6_HU... AN 1NDH Phosphoglycerate mutase-like APHA_ECOLI 1N8N HAD-like PPA_ZYMMO 1D2T Acid phosphatases PPA5_HUMAN 1UTE Metallo-dependent phosphatases PPAC_HUMAN 5PNT Phosphotyrosine protein phosphatases I PHOA_PENCH n/a n/a Cellulase (EC 3.2.1.4) GUNA_CLOCE 1EDG TIM beta/alpha-barrel GUNA_PSEFL 1UT9 Alpha/alpha toroid GUN1_STRHA 2BOD 7-Stranded beta/alpha barrel GUN_ASPAC 1KS4 Concanavalin A-like lectins/glucanases, GUNM_CLOTM 2FVG Phosphorylase/hydrolase-like GUNE_RUMFL 1L0H Predicted acyl carrier protein-like Superoxide dismutase (EC 1.15.1.1) SODF_ECOLI 1ISA Fe,Mn superoxide dismutase (SOD) SODC_ECOLI 1ESO Immunoglobulin-like beta-sandwich SODN_STRSO 1Q0D Four-helical up-and-down bundle NEC1_NICLS 2ET7 Double-stranded beta-helix Phosphoprotein (Ser) phosphatase (EC 3.1.3.16) PRP1_ECOLI 1G5B Metallo-dependent phosphatases PRPC_BACSU 1TXO PP2C-like CTDS1_HUMAN 1TA0 HAD-like DUS19_HUMAN 1M3G Phosphotyrosine protein phosphatases II Protein-tyrosine phosphatase (EC 3.1.3.48) PTPA_STRCO 1U2P Phosphotyrosine protein phosphatases I-like PTPRD_HUMAN 2FH7 Phosphotyrosine protein phosphatases II MPIP3_HUMAN 1QB0 Rhodanese/Cell cycle control phosphatase YWQE_BACSU 2ANU Predicted 7-stranded beta/alpha barrel EYA3_MOUSE 1JUD Predicted HAD-like DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) END3_ECOLI 2ABK DNA-glycosylase APEX1_HUMAN 1E9N DNase I-like APN1_YEAST 1QTW TIM beta/alpha-barrel FPG_ECOLI 1K82 MutM-like DNA repair proteins Adenylate cyclase (EC 4.6.1.1) CYA1_HUMAN 1CS4 P-loop NTPases O69199_AERHY 2ACA CYTH-like phosphatases CYAA_BORPE 1YRU EF Hand-like CYAA_ECOLI n/a n/a Inorganic pyrophosphatase (EC 3.6.1.1) IPYR_ARATH 1TWL OB-fold PPAC_BACSU 1WPM DHH phosphoesterases PPAX_BACSU 2HDO HAD-like AVP1_ARATH n/a Integral membrane protein, H + -transporting Catalase (EC 1.11.1.6) CATA_HUMAN 1QQW Heme-dependent catalase-like CATA_ECOLI 2FXG Heme-dependent peroxidases MCAT_LACPL 1JKU Ferritin-like Peroxidase (EC 1.11.1.7) PRDX6_MOUSE 1PRX Thioredoxin fold PERM_HUMAN 1MYP Heme-dependent peroxidases YCDB_ECOLI 2d3q Ferredoxin-like Chloride peroxidase (EC 1.11.1.10) PRXC_PSEPY 1A88 Alpha/beta-hydrolases PRXC_CURIN 1VNC Acid phosphatase PRXC_CALFU 2CPO EF Hand-lik Peroxiredoxin (EC 1.11.1.15) TDXH_AERPE 2E2G Thioredoxin fold AHPD_MYCTU 1KNC AhpD-like OSMC_ECOLI 1NYE OsmC-like Licheninase (EC 3.2.1.73) GUB_NICPL 2CYG TIM beta/alpha-barrel GUB_BACSU 1GBG Concanavalin A-like lectins/glucanases, GUB_BACCI 1V5C Alpha/alpha toroid Figure 3 Distribution of non-homologous isofunctional enzymes by COG functional categories .

Publication Year: 2010


Octarellin VI: using rosetta to design a putative artificial (?/?)8 protein.

(2013) PLoS One 8

PubMed: 23977165 | PubMedCentral: PMC3747059 | DOI: 10.1371/journal.pone.0071858

The PDB codes of the eighteen proteins are: 1A53, 1AJ2, 1B54, 1BQC, 1CNV, 1EDG, 1EOK, 1G0C, 1I1W, 1J6O, 1NQ6, 1O1Z, 1PYF, 1UJP, 1VFL, 1WDP, 2CYG, and 7A3H.

Publication Year: 2013


Structure of allergens and structure based epitope predictions.

(2014) Methods 66

PubMed: 23891546 | PubMedCentral: PMC3969231 | DOI: 10.1016/j.ymeth.2013.07.024

B Yellow lupine Lupinus luteus 2QIM [189] 

 Tryp_alpha_amyl (PF00234): Protease inhibitor/seed storage/lipid transfer proteins (LTP) family Ara h 2 Peanut Arachis hypogaea 3OB4 [10] A... a h 6 Peanut Arachis hypogaea 1W2Q [30] Ber e 1 Brazilian nut Bertholletia excelsa 2LVF [190] Bra n 1 Rapeseed Brassica napus 1PNB [191] Hor v 1 Barley Hordeum vulgare 1JTB, 1BE2 [192,193] Pru p 3 Peach Prunus persica 2ALG, 2B5S [46] Ric c 3 Castor bean Ricinus communis 1PSY [43] Zea m 14 Corn Zea mays 1MZL, 1MZM, 1FK0–7 1AFH [194–196] 

 Cupin_1 (PF00190): Cupin superfamily Ara h 1 Peanut Arachis hypogaea 3S7E, 3S7I, 3SMH [197–199] Ara h 3 Peanut Arachis hypogaea 3C3 V [200,201] Gly m 6.0101 Soybean Glycine max 1FXZ [202] Gly m 6.0501 Soybean Glycine max 1OD5, 2D5F, 2D5H [203,204] Gly m conglycinin Soybean Glycine max 1IPK, 1IPJ [205] Pru du 6 Almond Prunus dulcis 3FZ3 [206,207] 

 Lipocalin (PF00061): Lipocalin/cytosolic fatty-acid binding protein family Arg R 1 Pigeon tick Argas reflexus 2X46, 2X45 - Bla g 4 German cockroach Blattella germanica 3EBK [55] Bos d 2 Cow Bos taurus 1BJ7 [208] Bos d 5 Cow Bos taurus 1BSO [209] Can f 2 Dog Canis familiaris 3L4R [54] Der f 13 House dust mite Dermatophagoides farinae 2A0A [210] Equ c 1 Horse Equus caballus 1EW3 [211,212] Mus m 1 Mouse Mus musculus 1MUP, 1JV4 1DF3 [213–215] Per a 4 American cockroach Periplaneta americana 3EBW [55] Rat n 1 Rat (urine) Rattus norvegicus 2A2U, 2A2G [216] 

 EF hand (PF00036): EF hand family Bet v 4 White birch Betula verrucosa 1H4B [31] Che a 3 Lamb’s Quarters, White goosefoot Chenopodium album 2OPO [62] Cyp c 1 Carp Cyprinus carpio 4CPV, 5CPV and other∗ [58,59] Phl p 7 Timothy-grass Phleum pratense 1K9U 2LVK, 2LVJ, 2LVI {Verdino, 2002 #13 [63] 

 Peptidase_C1 (PF00112): Papain-like cysteine protease Act d 1 Kiwi fruit Actinidia delicionsa 2ACT, 1AEC [217–219] Car p 1 Papaya Carica papaya 1PPN, 1KHQ [220,221] Der p 1 House dust mite Dermatophagoides pteronyssinus 1XKG, 2AS8, 3F5 V, 3RVX, 3RVW [66,115,222] Der f 1 House dust mite Dermatophagoides farinae 3D6S, 3RVV [115,223] 

 Profilin (PF00235): Profilin family Ara h 5 Peanut Arachis hypogaea 4ESP [224] Ara t 8 Mouse-ear crest Arabidopsis thaliana 1A0 K [225] Bet v 2 White birch Betula verrucosa 1CQA [226] Hev b 8 Latex Hevea brasiliensis 1G5U - Thaumatin (PF00314): Thaumatin-like protein Act d 2 Kiwi fruit Actinidia deliciosa 4BCT - Mal d 2 Apple Malus x domestica 3ZS3 - Mus a 4 Banana Musa acuminata 1Z3Q [74] Pru av 2 Sweet cherry Prunus avium 2AHN [73] 

 Pollen_allerg_1 (PF01357): Expansin, C-terminal domain Phl p 1 (C-term domain) Timothy-grass Phleum pratense 1N10 [78] Phl p 2 Timothy-grass Phleum pratense 1WHO, 1WHP, 2VXQ 1BMW [15,81] Phl p 3 Timothy-grass Phleum pratense 3FT1, 3FT9 2JNZ [80] Zea m 1 (C-term domain) Corn Zea mays 2HCZ [79] 

 DPBB_1 (PF03330): rare lipoprotein A (RlpA)-like double-psi beta-barrel; Expansin, N-terminal domain Phl p 1 (N-term domain) Timothy-grass Phleum pratense 1N10 [78] Zea m 1 (N-termn domain) Corn Zea mays 2HCZ [79] 

 Pollen_allerg_2 (PF01620): Ribonuclease; Group 5/6 grass pollen allergen Phl p 5b Timothy-grass Phleum pratense 1L3P [83] Phl p 6 Timothy-grass Phleum pratense 1NLX - 

 Blo-t-5 (PF11642): Group 5/21 mite allergen Blo t 5 Storage mite Blomia tropicalis 2JMH, 2JRK [27,29] Der p 5 House dust mite Dermatophagoides pteronyssinus 3MQ1 [84,227] Blo t 21 Storage mite Blomia tropicalis 2LM9 [228] 

 CAP (PF00188): CRISP; PR-1; antigen 5 (Ag5) Sol i 3 Fire ant Solenopsis invicta 2VZN [229] Ves v 5 Common wasp Vespula vulgaris 1QNX [87] 

 Chitin_bind_1 (PF00187): Chitin recognition protein; Hevein-like domain Hev b 6.02 Latex Hevea brasiliensis 1WKX, 1Q9B 1HEV, 1T0 W [89,230] Tri a 18 Wheat Triticum aestivum 1WGC, 2CWG, 7WGA, 9WGA, 2UVO, 4AML, 2X3T [231–233] 

 E1_DerP2_DerF2 (PF02221): MD-2-related lipid-recognition (ML) domain; Group 2 mite allergen Der f 2 House dust mite Dermatophagoides farinae 1XWV, 2F08 1AHK, 1AHM, 1WRF [93,94,234,235] Der p 2 House dust mite Dermatophagoides pteronyssinus 1KTJ 1A9 V [90,92] 

 Glyco_hydro_17 (PF00332): Glycosyl hydrolases family 17/endo-1,3-beta-glucosidase Hev b 2 Latex Hevea brasiliensis 3EM5, 3F55 - Mus a 5 Banana Musa acuminata 2CYG [96] 

 Glyco_hydro_56 (PF01630): Hyaluronidase Api m 2 Honey bee Apis mellifera 1FCQ, 1FCU, 1FCV, 2J88 [98,120] Ves v 2 Common wasp Vespula vulgaris 2ATM [99] 

 Pro_isomerase (PF00160): Cyclophilin type peptidyl-prolyl cis–trans isomerase/CLD Asp f 11 Mold Aspergillus fumigatus 2C3B [105] Mala s 6 Mold Malassezia sympodialis 2CFE [104] 

 FAD linked oxidase (PF01565) / BBE-like (PF08031) Cyn d 4 Bermuda grass Cynodon dactylon 4DNS [106] Phl p 4 Timothy-grass Phleum pratense 3TSH, 3TSJ [107] Many parvalbumin structures have been solved (37 PDB entries currently) comprising proteins from 9 different species (from fish to human).

Publication Year: 2014