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Yorodumi- PDB-4kyo: Alanine-glyoxylate aminotransferase variant K390A in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kyo | ||||||
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Title | Alanine-glyoxylate aminotransferase variant K390A in complex with the TPR domain of human Pex5p | ||||||
Components |
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Keywords | TRANSFERASE/TRANSPORT PROTEIN / TPR-domain / aminotransferase / pyruvate / transport / peroxisomal import / primary hyperoxaluria / peroxisome / TRANSFERASE-TRANSPORT PROTEIN complex | ||||||
Function / homology | Function and homology information 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 / oxalic acid secretion / serine-pyruvate transaminase / protein targeting to peroxisome / alanine-glyoxylate transaminase / peroxisome matrix targeting signal-1 binding ...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 / oxalic acid secretion / serine-pyruvate transaminase / protein targeting to peroxisome / alanine-glyoxylate transaminase / peroxisome matrix targeting signal-1 binding / glyoxylate metabolic process / glycine biosynthetic process, by transamination of glyoxylate / L-alanine catabolic process / serine-pyruvate transaminase activity / 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 / alanine-glyoxylate transaminase activity / cerebral cortex neuron differentiation / cell development / L-serine metabolic process / pexophagy / L-cysteine catabolic process / positive regulation of multicellular organism growth / glyoxylate catabolic process / Glyoxylate metabolism and glycine degradation / endoplasmic reticulum organization / mitochondrial membrane organization / peroxisomal membrane / transaminase activity / neuromuscular process / amino acid binding / fatty acid beta-oxidation / cerebral cortex cell migration / peroxisomal matrix / negative regulation of protein-containing complex assembly / Notch signaling pathway / Pexophagy / Peroxisomal protein import / protein tetramerization / neuron migration / small GTPase binding / cellular response to reactive oxygen species / peroxisome / : / pyridoxal phosphate binding / E3 ubiquitin ligases ubiquitinate target proteins / intracellular membrane-bounded organelle / Golgi apparatus / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Fodor, K. / Lou, Y. / Wilmanns, M. | ||||||
Citation | Journal: Traffic / Year: 2015 Title: Ligand-Induced Compaction of the PEX5 Receptor-Binding Cavity Impacts Protein Import Efficiency into Peroxisomes. Authors: Fodor, K. / Wolf, J. / Reglinski, K. / Passon, D.M. / Lou, Y. / Schliebs, W. / Erdmann, R. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kyo.cif.gz | 283.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kyo.ent.gz | 226.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kyo_validation.pdf.gz | 496.4 KB | Display | wwPDB validaton report |
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Full document | 4kyo_full_validation.pdf.gz | 509.9 KB | Display | |
Data in XML | 4kyo_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 4kyo_validation.cif.gz | 79.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/4kyo ftp://data.pdbj.org/pub/pdb/validation_reports/ky/4kyo | HTTPS FTP |
-Related structure data
Related structure data | 4kxkC 3r9aS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 43132.863 Da / Num. of mol.: 2 / Mutation: K390A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGXT, AGT1, SPAT / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase #2: Protein | Mass: 36130.664 Da / Num. of mol.: 2 / Fragment: TPR domain, UNP residues 315-639 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PEX5, PXR1 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P50542 |
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-Non-polymers , 4 types, 725 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-BME / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 0.1 M Bis-Tris (pH=5.3), 0.12 M LiSO4, 17% (w/w) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.812 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 22, 2011 |
Radiation | Monochromator: HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.812 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→51.03 Å / Num. obs: 73170 / Redundancy: 2.6 % / Rmerge(I) obs: 0.114 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3R9A Resolution: 2.2→19.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.539 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.249 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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