Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 4

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

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 hydroca... bon 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


Combining docking with pharmacophore filtering for improved virtual screening.

(2009) J Cheminform 1

PubMed: 20298524 | PubMedCentral: PMC3152774 | DOI: 10.1186/1758-2946-1-6

There is only one holo C1 domain crystal structure ( 1PTR ) available in the PDB, with phorbol ester (a natural tumor promoter and DAG mimetic) in the binding site [ 32 ].

Publication Year: 2009


Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1.

(2013) Elife 2

PubMed: 23908768 | PubMedCentral: PMC3728621 | DOI: 10.7554/eLife.00813

( A ) The C1 domain of RasGRP1 (middle) is structurally similar to the C1 domain of PKCδ (PDB ID: 1PTR), shown here bound to a diacylglycerol mimic (phorbol ester) (yellow) (left).

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4140453

Figure 1 (A) Superimposed structures of the PKCα C1A domain (a homology model; red), the PKCα C1B domain (PDB code: 2ELI; green), and the ligand-bound PKCδ C1B domain (PDB code... 1PTR; gray).

The PKCα C1A model (residue 37–86, Figure 1 ) was generated by the homology-modeling server SWISS-MODEL, 52 with 42% sequence identity to the template (PDB code: 1PTR).

The PMA-bound models were built according to alignment of the ligand-bound PKCδ C1B structure (PDB code: 1PTR) to the protein structure in the above-mentioned models, followed by modification of the phorbol ester ligand to PMA.

Publication Year: 2014