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- PDB-8umg: Chromodomains of human CHD1 complexed with UNC10142 -

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Basic information

Entry
Database: PDB / ID: 8umg
TitleChromodomains of human CHD1 complexed with UNC10142
ComponentsChromodomain-helicase-DNA-binding protein 1
KeywordsPEPTIDE BINDING PROTEIN / CHD1 / Chromodomain-Helicase DNA-binding 1 / Methyllysine Reader
Function / homology
Function and homology information


nucleosome organization / ATP-dependent chromatin remodeler activity / positive regulation by host of viral transcription / nuclear chromosome / : / DNA helicase / Estrogen-dependent gene expression / histone binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity ...nucleosome organization / ATP-dependent chromatin remodeler activity / positive regulation by host of viral transcription / nuclear chromosome / : / DNA helicase / Estrogen-dependent gene expression / histone binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromatin remodeling / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain ...CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Chromodomain-helicase-DNA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGraboski, A.L. / Redinbo, M.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)5R33DA047023-05 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5R33DA047023-05 United States
CitationJournal: To Be Published
Title: Optimization of a quinazoline-based scaffold against human CHD1
Authors: Johnson, R.L. / Graboski, A.L. / Walton, W.G. / James, L.I. / Redinbo, M.R.
History
DepositionOct 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromodomain-helicase-DNA-binding protein 1
B: Chromodomain-helicase-DNA-binding protein 1
C: Chromodomain-helicase-DNA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6737
Polymers66,4403
Non-polymers1,2334
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.531, 55.193, 101.095
Angle α, β, γ (deg.)90.000, 112.779, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Chromodomain-helicase-DNA-binding protein 1 / CHD-1 / ATP-dependent helicase CHD1


Mass: 22146.762 Da / Num. of mol.: 3 / Mutation: +KK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O14646
#2: Chemical ChemComp-X31 / 1-{4-[{2-(azonan-1-yl)-6-methoxy-7-[3-(piperidin-1-yl)propoxy]quinazolin-4-yl}(methyl)amino]piperidin-1-yl}ethan-1-one


Mass: 580.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H52N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG3350, sodium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2023
RadiationMonochromator: Double Crystal Monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→55.34 Å / Num. obs: 10543 / % possible obs: 98.72 % / Redundancy: 3.4 % / Biso Wilson estimate: 7.88 Å2 / CC1/2: 0.937 / CC star: 0.984 / Net I/σ(I): 1.94
Reflection shellResolution: 3.1→3.21 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 962 / CC1/2: 0.107 / CC star: 0.44 / % possible all: 92.32

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→55.34 Å / SU ML: 0.4988 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.1892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.32 1042 9.97 %
Rwork0.2381 9410 -
obs0.2465 10452 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.52 Å2
Refinement stepCycle: LAST / Resolution: 3.1→55.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 86 99 3635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013627
X-RAY DIFFRACTIONf_angle_d1.34964914
X-RAY DIFFRACTIONf_chiral_restr0.0674491
X-RAY DIFFRACTIONf_plane_restr0.0069634
X-RAY DIFFRACTIONf_dihedral_angle_d19.7922513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.270.38271360.29821261X-RAY DIFFRACTION93.26
3.27-3.470.31991500.24971331X-RAY DIFFRACTION99.4
3.47-3.740.35451480.25051341X-RAY DIFFRACTION99.73
3.74-4.110.30851510.22851352X-RAY DIFFRACTION99.87
4.11-4.710.25721490.19911350X-RAY DIFFRACTION99.87
4.71-5.930.34151530.21891373X-RAY DIFFRACTION99.87
5.93-55.340.31191550.24681402X-RAY DIFFRACTION99.05
Refinement TLS params.Method: refined / Origin x: 12.2880707602 Å / Origin y: -0.0752440390888 Å / Origin z: 23.7559971228 Å
111213212223313233
T0.0376484664232 Å20.0182949094863 Å2-5.50172476891E-5 Å2-0.0354328512736 Å2-0.0171726449778 Å2--0.0456240220269 Å2
L0.522841122695 °2-0.114277097277 °2-0.0896301073173 °2-0.325954163501 °2-0.12797469246 °2---0.00318384744374 °2
S-0.00993199980553 Å °0.0329708208036 Å °0.0327073867512 Å °-0.0555922990286 Å °-0.00179003967222 Å °-0.0240641666138 Å °0.0494414182146 Å °-0.0087776219336 Å °-0.00821672079841 Å °
Refinement TLS groupSelection details: all

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