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- PDB-4u6q: CtBP1 bound to inhibitor 2-(hydroxyimino)-3-phenylpropanoic acid -

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Basic information

Entry
Database: PDB / ID: 4u6q
TitleCtBP1 bound to inhibitor 2-(hydroxyimino)-3-phenylpropanoic acid
ComponentsC-terminal-binding protein 1
KeywordsOXIDOREDUCTASE / Rossman fold / transcription regulator / cancer / inhibitor
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 / SUMOylation of transcription cofactors / transcription corepressor binding / Deactivation of the beta-catenin transactivating complex / transcription coregulator binding / 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
C-terminal binding protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain ...C-terminal binding protein / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2E)-2-(hydroxyimino)-3-phenylpropanoic acid / FORMIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / C-terminal-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHilbert, B.J. / Morris, B.L. / Ellis, K.C. / Paulsen, J.L. / Schiffer, C.A. / Grossman, S.R. / Royer Jr., W.E.
CitationJournal: 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
DepositionJul 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-terminal-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0705
Polymers38,1391
Non-polymers9314
Water3,153175
1
A: C-terminal-binding protein 1
hetero molecules

A: C-terminal-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,14010
Polymers76,2792
Non-polymers1,8618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/31
Buried area8510 Å2
ΔGint-64 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.000, 84.000, 159.472
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

21A-540-

HOH

31A-571-

HOH

41A-572-

HOH

51A-573-

HOH

61A-574-

HOH

71A-671-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein C-terminal-binding protein 1 / CtBP1


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, 179 molecules

#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-3CR / (2E)-2-(hydroxyimino)-3-phenylpropanoic acid


Mass: 179.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 42.23 % / Description: bi-pyramidal crystal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 75 mM CaCl2, 100 mM Hepes pH 7.5, and 1 mM NADH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.99 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 15487 / Num. obs: 15450 / % possible obs: 99.66 % / Redundancy: 18.1 % / Biso Wilson estimate: 39.34 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 31.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 5.48 / % possible all: 99.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LCE

4lce


Resolution: 2.3→30 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 771 4.99 %Random selection
Rwork0.2042 ---
obs0.2063 15450 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 61 175 2680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042554
X-RAY DIFFRACTIONf_angle_d0.8363475
X-RAY DIFFRACTIONf_dihedral_angle_d16.214917
X-RAY DIFFRACTIONf_chiral_restr0.045411
X-RAY DIFFRACTIONf_plane_restr0.003447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44290.29181250.24762382X-RAY DIFFRACTION100
2.4429-2.63140.27441130.24242401X-RAY DIFFRACTION100
2.6314-2.8960.29731410.23562385X-RAY DIFFRACTION100
2.896-3.31460.32811290.21782412X-RAY DIFFRACTION100
3.3146-4.17430.20291270.18342464X-RAY DIFFRACTION100
4.1743-30.02090.21921360.18952635X-RAY DIFFRACTION100

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