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- PDB-5khh: HCN2 CNBD in complex with inosine-3', 5'-cyclic monophosphate (cIMP) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5khh | ||||||
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Title | HCN2 CNBD in complex with inosine-3', 5'-cyclic monophosphate (cIMP) | ||||||
![]() | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 | ||||||
![]() | TRANSPORT PROTEIN / protein-ligand complex / cycilc nucleotide binding domain / ion transport | ||||||
Function / homology | ![]() HCN channels / HCN channel complex / cellular response to cGMP / regulation of membrane depolarization / intracellularly cAMP-activated cation channel activity / sodium ion import across plasma membrane / voltage-gated sodium channel activity / voltage-gated potassium channel activity / potassium ion import across plasma membrane / sodium ion transmembrane transport ...HCN channels / HCN channel complex / cellular response to cGMP / regulation of membrane depolarization / intracellularly cAMP-activated cation channel activity / sodium ion import across plasma membrane / voltage-gated sodium channel activity / voltage-gated potassium channel activity / potassium ion import across plasma membrane / sodium ion transmembrane transport / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / somatodendritic compartment / dendrite membrane / dendritic shaft / PDZ domain binding / regulation of membrane potential / molecular adaptor activity / axon / neuronal cell body / dendrite / protein-containing complex binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ng, L.C.T. / Putrenko, I. / Baronas, V. / Van Petegem, F. / Accili, E.A. | ||||||
![]() | ![]() Title: Cyclic Purine and Pyrimidine Nucleotides Bind to the HCN2 Ion Channel and Variably Promote C-Terminal Domain Interactions and Opening. Authors: Ng, L.C. / Putrenko, I. / Baronas, V. / Van Petegem, F. / Accili, E.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.2 KB | Display | ![]() |
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PDB format | ![]() | 42.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 734.1 KB | Display | ![]() |
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Full document | ![]() | 735.9 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5khgC ![]() 5khiC ![]() 5khjC ![]() 5khkC ![]() 1q5oS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23883.330 Da / Num. of mol.: 1 / Fragment: UNP residues 443-643 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-6SW / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 200 mM NaCl, 0.1 mM sodium citrate pH 5.5, 14.5% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2012 / Details: 1000 um thick sensor | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97944 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→44.12 Å / Num. obs: 26044 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 9.83 % / Biso Wilson estimate: 42.756 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.06 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1Q5O Resolution: 1.77→44.12 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.738 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.13 / Details: molecular replacement
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.67 Å2 / Biso mean: 36.579 Å2 / Biso min: 21.85 Å2
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Refinement step | Cycle: final / Resolution: 1.77→44.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.771→1.817 Å / Total num. of bins used: 20
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