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- PDB-1fch: CRYSTAL STRUCTURE OF THE PTS1 COMPLEXED TO THE TPR REGION OF HUMA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fch | ||||||
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Title | CRYSTAL STRUCTURE OF THE PTS1 COMPLEXED TO THE TPR REGION OF HUMAN PEX5 | ||||||
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![]() | SIGNALING PROTEIN / PROTEIN-PEPTIDE COMPLEX / TETRATRICOPEPTIDE REPEAT / TPR / HELICAL REPEAT | ||||||
Function / homology | ![]() protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / protein targeting to peroxisome / peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix / protein import into peroxisome matrix, docking ...protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / protein targeting to peroxisome / peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix / protein import into peroxisome matrix, docking / protein carrier chaperone / very long-chain fatty acid metabolic process / cerebral cortex neuron differentiation / cell development / pexophagy / positive regulation of multicellular organism growth / endoplasmic reticulum organization / mitochondrial membrane organization / peroxisomal membrane / neuromuscular process / fatty acid beta-oxidation / cerebral cortex cell migration / peroxisomal matrix / negative regulation of protein-containing complex assembly / Pexophagy / Peroxisomal protein import / protein tetramerization / neuron migration / small GTPase binding / cellular response to reactive oxygen species / peroxisome / E3 ubiquitin ligases ubiquitinate target proteins / Golgi apparatus / enzyme binding / protein-containing complex / mitochondrion / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Gatto Jr., G.J. / Geisbrecht, B.V. / Gould, S.J. / Berg, J.M. | ||||||
![]() | ![]() Title: Peroxisomal targeting signal-1 recognition by the TPR domains of human PEX5. Authors: Gatto Jr., G.J. / Geisbrecht, B.V. / Gould, S.J. / Berg, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.6 KB | Display | ![]() |
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PDB format | ![]() | 103.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.8 KB | Display | ![]() |
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Full document | ![]() | 451.6 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 |
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40989.910 Da / Num. of mol.: 2 / Fragment: C-TERMINAL TPR REGION Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 638.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.29 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Sodium HEPES, Sodium Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: peptide solution was diluted 1:1 with reservoir | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 9, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 38298 / Num. obs: 38298 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.227 / Num. unique all: 1916 / % possible all: 98.8 |
Reflection shell | *PLUS % possible obs: 98.8 % / Mean I/σ(I) obs: 5.9 |
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Processing
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Refinement | Resolution: 2.2→29.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2170352.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.56 Å2 / ksol: 0.351 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→29.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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