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PDB ID Mentions in PubMed Central Article count: 2

Citations in PubMed

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PDB ID Mentions in PubMed Central

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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 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] Chole... terol 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).

Experiment a Calculation b Protein name PDB id Residues buried from water or important for membrane binding Method References Δ G calc (kcal/mol) D (Å) Residues penetrating the hydrocarbon membrane core Lipid clamps (specific binding of lipid ligands) C2 domain of phospholipase A2 1rlw A34, F35, G36, M38, L39, Y96, V97, M98 Bn, SL [6, 84, 85] -7.1 5.3 A34, F35, G36, M38, L39, Y96, V97, M98 C2A domain of synaptotagmin I 1byn M173, G174, F234 Bn, SL [7, 86] -4.4 3.7 M173, G174, F234 C2 domain of protein knase Cα 1dsy N189 , R249 , R252 SL [8] -2.0 1.5 P188, N189 , T250 C2B domain of synaptotagmin I 1uov G305, I367 SL [9] -4.3 2.4 V304, G305, I367 , G368 C2 domain of protein kinase Cε 1gmi I89 , Y91 Bn [87] -5.1 2.4 V29, P31, I89 PX domain (p40phox) 1h6h F35, Y94, V95 Bn [39] -4.5 3.2 F35, Y94, V95 PX domain (p47phox) 1o7k W80 Bn [39] -1.9 1.4 W80 FYVE domain of EEA1 1hyi V21, T22 NMR [40] -2.9 2.5 V21, T22 FYVE domain of Vps27p 1vfy L185, L186 Bn [88] -4.0 2.9 L185, L186 C1 domain of protein kinase Cδ 1ptr W252, L254, V255 Bn [89] -5.7 6.8 M239, P241, L250, W252 , G253, L254, V255 Epsin ENTH domain 1h0a L6, M10 Bn [77] -5.2 2.9 L6, M10 , I13, V14 Discoidin domain of factor V 1czs W26, W27 Bn [90] -3.0 4.2 W26, W27 , L79, and S80 Discoidin domain of factor Va 1sdd Y1956, L1957, W2063, W2064 Bn [91] -5.6 3.3 Y1956, L1957, W2063, W2064 Discoidin domain of factor VIII 1d7p M2199, F2200, L2251, L2252 Bn [92] -8.1 3.9 M2199, F2200, L2251, L2252 Annexin V 1a8a T72 , S144 , W185 , S228 , S303 SL [93] -6.3 2.5 L29, T72 , A101, W185 , A260 Annexin XII 1dm5 E142 , S144 , G145 SL [94] -8.3 3.1 I29, L101, I185 Equinatoxin II 1iaz W112 NMR [95] -2.2 3.1 P81, V82, W112 Other proteins Prostaglandin H2 synthase 1 1q4g I74, W75, W77, L78, F88, F91, L92, W98, L99, F102 Bn, Fn [96] -37.8 7.2 I74, W75, W77, L78 , T81, L82, F88, F91, L92, W98, L99, F102 , V103, T106, F107, I108 Antimicrobial peptide kalata B1 1nb1 W19-V21, L27-V29 NMR [97] -5.4 5.2 W19-V21 , L27-V29 Pancreatic phospholipase A 2 , group IB 4p2p W3 Flq [11] -8.7 3.5 W3 , H17, L19, M20, L64, V65 Bee venom phospholipase A 2 1poc I2 , K14 , I78 SL* [42] -10.3 5.7 I1, I2 , Y3, P4, G5, I78 , F82, M86, L90 Human secretory phospholipase A 2 , group IIa 1n28 V3 , K10 , L19, F23, F63 SL* [43] -6.6 4.8 V3, L19, F23, F63 Snake venom phospholipase A 2 , group I 1poa W61, F64 , Y110 Bn [98] -5.4 4.5 Y3, W18, W19, W61, F64 Snake venom phospholipase A 2 , group II 1vap W20 , W30, W109 FL [99] -10.2 4.3 F3, M13, L19, W30 , M61, W109 Snake venom phospholipase A 2 , group IIB 1jia Y120 , P121, I124 , L125 Bn [100] d -8.7 3.1 V20, F24, A119, P121, I124 Phospholipase C 2ptd I43, W47, W242 Bn [101] -6.0 3.9 P42, I43 , W47 , T240, A241, W242 α-toxin (bacterial phospholipase C) 1ca1 Y331, F334 Fn [102] -4.5 2.2 V143, A146, M210, W214, Y331, F334 15-lipoxygenase 1lox Y15 , F70 , L71 , W181 c , L195 Bn [103] -7.4 6.3 L71 , I194, L195 , L291, Y292, F412 8R-lipoxygenase 1zq4 W413, W449 FL, Fn [104] -5.0 5.9 W413 , F414, Y448, W449 , V560, M570 Cholesterol oxidase 1coy M81 FLq [105] -4.1 5.3 M81 , M332, W333, L369, Y372 Signal peptidase 1kn9 W300 Fn [106] -4.5 4.5 W300 , M301, F303, L314, L316 Synapsin I 1auv Regions 166–192, 233–258, 278–327 CL [107] -4.4 2.5 L168, V172, L297 α-synuclein 1xq8 T59, V63, G67, V70, V74, V77, T81, A85, A89 SL [108] -22.8 17.9 T59, V63 , V66, G67 , V70, V74, V77 , A78, T81, A85 , I88, A89 Perfringolysin 1pfo W466 Bn [109] -5.5 3.4 L462, W466 , L491, Y492 Daptomycin 1t5n Kyn14 FL [110] -9.8 4.9 Dka1, W2, Kyn14 Lactoferricin B 1lfc W6, W8 FL [111] -4.6 5.3 W6, W8 , L13-P16, I18 Hanatoxin 1d1h W30 FLq [112] -2.5 3.9 Y4, L5, F6, W30 Subtilosin 1pxq W34 FL [113] -6.7 5.1 F22, F31, W34 a Bn – based on membrane binding affinities of mutants; SL – spin-labeling data based on depth parameters Φ (SL* – based only on exposure of labels to polar probes); FL – fluorescence; FLq – fluorescence quenching; Fn – functional studies of mutants; CL – chemical labeling.

Publication Year: 2007


Modeling of human factor Va inactivation by activated protein C.

(2012) BMC Syst Biol 6

PubMed: 22607732 | PubMedCentral: PMC3403913 | DOI: 10.1186/1752-0509-6-45

In all three simulations, the FVa domain orientation is based on the crystal structure of bovine inactivated FVa i (FVa 1-306 FVa LC ) solved by Adams et al. [PDB ID: 1SDD] [ 56 ].

Publication Year: 2012