Primary Citation PubMed: 7781068
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
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.
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  -2.0 1.5 P188, N189 , T250 C2B domain of synaptotagmin I 1uov G305, I367 SL  -4.3 2.4 V304, G305, I367 , G368 C2 domain of protein kinase Cε 1gmi I89 , Y91 Bn  -5.1 2.4 V29, P31, I89 PX domain (p40phox) 1h6h F35, Y94, V95 Bn  -4.5 3.2 F35, Y94, V95 PX domain (p47phox) 1o7k W80 Bn  -1.9 1.4 W80 FYVE domain of EEA1 1hyi V21, T22 NMR  -2.9 2.5 V21, T22 FYVE domain of Vps27p 1vfy L185, L186 Bn  -4.0 2.9 L185, L186 C1 domain of protein kinase Cδ 1ptr W252, L254, V255 Bn  -5.7 6.8 M239, P241, L250, W252 , G253, L254, V255 Epsin ENTH domain 1h0a L6, M10 Bn  -5.2 2.9 L6, M10 , I13, V14 Discoidin domain of factor V 1czs W26, W27 Bn  -3.0 4.2 W26, W27 , L79, and S80 Discoidin domain of factor Va 1sdd Y1956, L1957, W2063, W2064 Bn  -5.6 3.3 Y1956, L1957, W2063, W2064 Discoidin domain of factor VIII 1d7p M2199, F2200, L2251, L2252 Bn  -8.1 3.9 M2199, F2200, L2251, L2252 Annexin V 1a8a T72 , S144 , W185 , S228 , S303 SL  -6.3 2.5 L29, T72 , A101, W185 , A260 Annexin XII 1dm5 E142 , S144 , G145 SL  -8.3 3.1 I29, L101, I185 Equinatoxin II 1iaz W112 NMR  -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  -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  -5.4 5.2 W19-V21 , L27-V29 Pancreatic phospholipase A 2 , group IB 4p2p W3 Flq  -8.7 3.5 W3 , H17, L19, M20, L64, V65 Bee venom phospholipase A 2 1poc I2 , K14 , I78 SL*  -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*  -6.6 4.8 V3, L19, F23, F63 Snake venom phospholipase A 2 , group I 1poa W61, F64 , Y110 Bn  -5.4 4.5 Y3, W18, W19, W61, F64 Snake venom phospholipase A 2 , group II 1vap W20 , W30, W109 FL  -10.2 4.3 F3, M13, L19, W30 , M61, W109 Snake venom phospholipase A 2 , group IIB 1jia Y120 , P121, I124 , L125 Bn  d -8.7 3.1 V20, F24, A119, P121, I124 Phospholipase C 2ptd I43, W47, W242 Bn  -6.0 3.9 P42, I43 , W47 , T240, A241, W242 α-toxin (bacterial phospholipase C) 1ca1 Y331, F334 Fn  -4.5 2.2 V143, A146, M210, W214, Y331, F334 15-lipoxygenase 1lox Y15 , F70 , L71 , W181 c , L195 Bn  -7.4 6.3 L71 , I194, L195 , L291, Y292, F412 8R-lipoxygenase 1zq4 W413, W449 FL, Fn  -5.0 5.9 W413 , F414, Y448, W449 , V560, M570 Cholesterol oxidase 1coy M81 FLq  -4.1 5.3 M81 , M332, W333, L369, Y372 Signal peptidase 1kn9 W300 Fn  -4.5 4.5 W300 , M301, F303, L314, L316 Synapsin I 1auv Regions 166–192, 233–258, 278–327 CL  -4.4 2.5 L168, V172, L297 α-synuclein 1xq8 T59, V63, G67, V70, V74, V77, T81, A85, A89 SL  -22.8 17.9 T59, V63 , V66, G67 , V70, V74, V77 , A78, T81, A85 , I88, A89 Perfringolysin 1pfo W466 Bn  -5.5 3.4 L462, W466 , L491, Y492 Daptomycin 1t5n Kyn14 FL  -9.8 4.9 Dka1, W2, Kyn14 Lactoferricin B 1lfc W6, W8 FL  -4.6 5.3 W6, W8 , L13-P16, I18 Hanatoxin 1d1h W30 FLq  -2.5 3.9 Y4, L5, F6, W30 Subtilosin 1pxq W34 FL  -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
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
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.