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- PDB-8gsj: APC-Asef tripeptide inhibitor -

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Basic information

Entry
Database: PDB / ID: 8gsj
TitleAPC-Asef tripeptide inhibitor
ComponentsAdenomatous polyposis coli proteinFamilial adenomatous polyposis
KeywordsPROTEIN BINDING/INHIBITOR / PROTEIN BINDING-INHIBITOR COMPLEX
Function / homology
Function and homology information


APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity ...APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity / negative regulation of microtubule depolymerization / negative regulation of cyclin-dependent protein serine/threonine kinase activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / microtubule plus-end binding / beta-catenin destruction complex / regulation of microtubule-based process / heart valve development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / catenin complex / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / endocardial cushion morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / mitotic cytokinesis / bicellular tight junction / lateral plasma membrane / Deactivation of the beta-catenin transactivating complex / adherens junction / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / kinetochore / ruffle membrane / beta-catenin binding / Wnt signaling pathway / positive regulation of protein catabolic process / cell migration / Ovarian tumor domain proteases / lamellipodium / insulin receptor signaling pathway / nervous system development / positive regulation of cold-induced thermogenesis / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / microtubule / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / centrosome / DNA damage response / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding ...Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
(1R,2S)-2-phenylcyclopropanamine / GLUTAMIC ACID / 2-methylsulfanylpyrimidine-4-carbaldehyde / LEUCINE / BETA-(2-NAPHTHYL)-ALANINE / Adenomatous polyposis coli protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsZhang, J. / Wang, X.F. / Song, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925034 China
CitationJournal: To Be Published
Title: APC-Asef tripeptide inhibitor
Authors: Zhang, J. / Wang, X.F. / Song, K.
History
DepositionSep 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenomatous polyposis coli protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,75012
Polymers37,4081
Non-polymers1,34111
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-6 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 66.480, 84.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenomatous polyposis coli protein / Familial adenomatous polyposis / Protein APC / Deleted in polyposis 2.5


Mass: 37408.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P25054

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Non-polymers , 8 types, 100 molecules

#2: Chemical ChemComp-K8C / 2-methylsulfanylpyrimidine-4-carbaldehyde


Mass: 154.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-NAL / BETA-(2-NAPHTHYL)-ALANINE


Type: L-peptide linking / Mass: 215.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Chemical ChemComp-GJZ / (1R,2S)-2-phenylcyclopropanamine / Tranylcypromine


Mass: 133.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25% w/v PEG 4000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→52.22 Å / Num. obs: 20548 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 1 / Net I/σ(I): 21.9
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 1652 / CC1/2: 0.852

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IZA

5iza


Resolution: 2.1→52.22 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.058 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1021 5 %RANDOM
Rwork0.1985 ---
obs0.2013 19480 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.55 Å2 / Biso mean: 60.471 Å2 / Biso min: 37.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2--4.08 Å2-0 Å2
3----5.22 Å2
Refinement stepCycle: final / Resolution: 2.1→52.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 86 89 2779
Biso mean--72.21 61.46 -
Num. residues----336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192738
X-RAY DIFFRACTIONr_bond_other_d0.0010.022655
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9793698
X-RAY DIFFRACTIONr_angle_other_deg0.93736100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4335337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37824.783115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45915495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7481515
X-RAY DIFFRACTIONr_chiral_restr0.060.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023062
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02615
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.43 67 -
Rwork0.362 1401 -
obs--98.52 %

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