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- PDB-6b42: Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) 2'-de... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6b42 | |||||||||
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Title | Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) 2'-deoxy-AMP complex at 1.13A resolution | |||||||||
![]() | Histidine triad nucleotide-binding protein 1 | |||||||||
![]() | HYDROLASE / HINT / histidine triad / HIT | |||||||||
Function / homology | ![]() purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Maize, K.M. / Finzel, B.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A Crystal Structure Based Guide to the Design of Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) Activated ProTides. Authors: Maize, K.M. / Shah, R. / Strom, A. / Kumarapperuma, S. / Zhou, A. / Wagner, C.R. / Finzel, B.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.8 KB | Display | ![]() |
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PDB format | ![]() | 43 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 721 KB | Display | ![]() |
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Full document | ![]() | 721 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5klyC ![]() 5klzC ![]() 5km0C ![]() 5km1C ![]() 5km2C ![]() 5km3C ![]() 5km4C ![]() 5km5C ![]() 5km6C ![]() 5km8C ![]() 5km9C ![]() 5kmaC ![]() 5kmbC ![]() 5wa8C ![]() 5wa9C ![]() 1av5S S: Starting model for refinement C: citing same article ( |
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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: 14096.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-D5M / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 100 MM MES, 33% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→70.566 Å / Num. obs: 43018 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 9.71 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.13→1.134 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 350 / CC1/2: 0.75 / % possible all: 79.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AV5 Resolution: 1.13→35.283 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.34 Å2 / Biso mean: 12.4083 Å2 / Biso min: 5.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.13→35.283 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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