+Open data
-Basic information
Entry | Database: PDB / ID: 4u6s | ||||||
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Title | CtBP1 in complex with substrate phenylpyruvate | ||||||
Components | C-terminal-binding protein 1 | ||||||
Keywords | OXIDOREDUCTASE / Rossman fold / transcription regulator / cancer / substrate | ||||||
Function / homology | Function and homology information Signaling by TCF7L2 mutants / Repression of WNT target genes / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex ...Signaling by TCF7L2 mutants / Repression of WNT target genes / synaptic vesicle clustering / presynaptic active zone cytoplasmic component / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / synaptic vesicle endocytosis / white fat cell differentiation / GABA-ergic synapse / transcription repressor complex / viral genome replication / transcription corepressor binding / SUMOylation of transcription cofactors / transcription coregulator binding / Deactivation of the beta-catenin transactivating complex / transcription corepressor activity / NAD binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of cell cycle / protein domain specific binding / negative regulation of cell population proliferation / protein phosphorylation / negative regulation of DNA-templated transcription / glutamatergic synapse / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hilbert, B.J. / Morris, B.L. / Ellis, K.C. / Paulsen, J.L. / Schiffer, C.A. / Grossman, S.R. / Royer Jr., W.E. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Structure-Guided Design of a High Affinity Inhibitor to Human CtBP. Authors: Hilbert, B.J. / Morris, B.L. / Ellis, K.C. / Paulsen, J.L. / Schiffer, C.A. / Grossman, S.R. / Royer, W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u6s.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u6s.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 4u6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u6s_validation.pdf.gz | 737.1 KB | Display | wwPDB validaton report |
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Full document | 4u6s_full_validation.pdf.gz | 738.1 KB | Display | |
Data in XML | 4u6s_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 4u6s_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/4u6s ftp://data.pdbj.org/pub/pdb/validation_reports/u6/4u6s | HTTPS FTP |
-Related structure data
Related structure data | 4u6qC 4lceS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38139.469 Da / Num. of mol.: 1 / Fragment: NAD nucleotide binding residues 28-353 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTBP1, CTBP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / Variant (production host): RIL+ References: UniProt: Q13363, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 5 types, 204 molecules
#2: Chemical | ChemComp-NAD / |
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#3: Chemical | ChemComp-PPY / |
#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-FMT / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 42.14 % / Description: Bi-pyramidal crystals |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 200 mM Calcium Chloride, 100 mM Hepes pH 7.5, 2.5 mM NAD+ |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.99 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→32 Å / Num. all: 19870 / Num. obs: 19617 / % possible obs: 98.44 % / Redundancy: 28 % / Rsym value: 0.074 / Net I/σ(I): 30.46 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 17 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 6.39 / % possible all: 94.64 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LCE Resolution: 2.1→30.004 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30.004 Å
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Refine LS restraints |
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LS refinement shell |
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