Citations in PubMed

Primary Citation PubMed: 6292726 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 2

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 role of hydrophobic interactions in positioning of peripheral proteins in membranes.

(2007) BMC Struct Biol 7

PubMed: 17603894 | PubMedCentral: PMC1934363 | DOI: 10.1186/1472-6807-7-44

Protein PDB id Δ G calc (kcal/mol) D (Å) Method a References Lipid clamps C1 domain of protein kinase Cγ 1tbn -2.3 7.5 NMR [114] Annexin 24 1dk5 -1.2 1.8 FL [115] Blood coagula... ion factor VIIa 1dan -5.7 4.8 FL [116] Seminal plasma protein 1h8p -12.3 9.2 EPR [117] Other proteins Cardiotoxin III 1h0j -13.1 6.5 FTIR [118] Cytotoxin 1 1tgx -12.4 6.8 FLq [119] Cardiotoxin II 1ffj -18.1 8.7 NMR [120] Sapecin 1l4v -6.6 6.1 NMR [121] Cytochrome c 1hrc -2.0 1.9 SL, NMR [122, 123] Coagulation factor IXa 1pfx -3.8 3.2 FL [124] Coagulation factor XIV 1lqv -4.9 3.5 FL [125] Peptides Alamethicin 1amt -23.7 28.1 NMR, SL [44–46] Zervamicin IIb 1ih9 -14.3 9.9 FL [47] Antiamoebin I 1joh -16.4 14.4 FL [47] Magainin 2mag -14.5 10.1 NMR, FL [126, 127] Nisin 1wco -4.0 8.8 NMR [128] Neuropeptide Y 1icy -9.4 9.4 SL [129] Mersacidin 1mqz -4.9 3.5 NMR [130] a As in Table 1; FTIR – ATR FTIR spectroscopy.

Protein name PDB id ΔG calc (kcal/mol) ΔG exp (kcal/mol) a Reference Predominantly nonspecific hydrophobic association Cholesterol oxidase ( Brevibacterium ) 1coy -4.1 -5.9 [105] Cholesterol oxidase ( Streptomyces ) 1b4v -7.1 -8.7 [151] 8R-lipoxygenase 1zq4 -5.0 -6.8 [104] Snake phospholipase A 2 , group I 1poa -5.4 -11.4 [98] Snake phospholipase A 2 , group II 1vap -10.2 -10.6 c [98] Human phospholipase A 2 , group II 1n28 -6.3 -6.4 [57] Voltage sensor toxin 1s6x -5.2 -6.8 [152] Kalata B1 1nb1 -5.4 -6.4 [153] Phospolipase C 2ptd -6.0 -5.6 [101] Insect phospholipase A 2 1poc -10.3 -8.2 [154] Human phospholipase A 2 , group X 1le6 -21.8 -6.1 [57] Octreotide -2 1soc -5.6 -5.4 [155] Pancreatic lipase 1ethA -16.1 -11.0 [156] Cytotoxin 1 1tgx -12.4 -9.6 [119] Sapecin 1l4v -6.6 -9.9 [121] C1 domain of Raf-1 kinase 1faq -8.1 -5.5 [2] Gramicidin S 1tk2 -14.1 -12.1 [157] Specific binding of lipid ligands (lipid clamps) C2 domain of cPLA 2 1rlw -7.1 -11.4 c [84] cPLA 2 holoenzyme 1cjy -9.8 -11.0 [158] Phospholipase Cδ1 1djx -3.2 -12.0 b [159] C2 domain of synaptotagmin IA 1byn -4.4 -6.5 [160] C2 domain of PKCβ 1a25 -2.2 -7.5 [160] C2 domain of PKCα 1dsy -0.6 -12.8 c [161] C2 domain of PTEN 1d5r -2.6 -9.7 [162] C2 domain coagulation factor Va 1sdd -5.6 -8.9 c [163] C2 domain coagulation factor VIII 1d7p -8.1 -11.2 [92] FYVE domain of Vps27 1vfy -4.0 -10.3 [164] ENTH domain of epsin 1h0a -5.2 -10.5 [77] PX domain (p40phox) 1h6h -4.5 -12.6 [39] PX domain (p47phox) 1o7k -2.7 -12.1 [39] PH domain of PLC-δ1 1mai -3.2 -6.2 [165] Equinatoxin II 1iaz -2.2 -11.1 [166] Predominantely nonspecific electrostatic binding Charybdotoxin 2crd -1.6 -3.6 [17] Mitochondrial cytochrome c 1hrc -2.0 -5.3 [76, 167] Helix-coil transitions during binding Magainin 2mag -14.5 -8.0 [168] Alamethicin 1amt -23.7 -6.2 [169] Zervamicin 1ih9 -14.3 -7.8 [47] Neuropeptide Y 1icy -9.4 -4.7 [125] a Experimental values were taken for lipid compositions that provided maximal binding affinity and at the ionic strength close to physiological conditions (~0.1 M of KCl).

Publication Year: 2007


Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases.

(2010) BMC Struct Biol 10

PubMed: 20067617 | PubMedCentral: PMC2835699 | DOI: 10.1186/1472-6807-10-1

Reductase domain-ligand docking The reductase substrates included linear peptides such as alamethicin ( 1AMT ), antiamoebin I ( 1GQ0 ), trichotoxin ( 1M24 ), chryospermin C ( 1EE7 ) and gramicidin ( 1... RM ) [ 36 - 39 ].

Publication Year: 2010