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- PDB-7ugl: Bromodomain of CBP liganded with BMS-536924 and SGC-CBP30 -

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Basic information

Entry
Database: PDB / ID: 7ugl
TitleBromodomain of CBP liganded with BMS-536924 and SGC-CBP30
ComponentsHistone acetyltransferase
KeywordsTRANSCRIPTION / bromodomain / small molecule ligand / complex
Function / homology
Function and homology information


histone acetyltransferase activity / histone acetyltransferase / transcription coregulator activity / nuclear body / regulation of DNA-templated transcription / nucleoplasm
Similarity search - Function
: / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. ...: / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-2LO / Chem-N6I / histone acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSchonbrunn, E. / Bikowitz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis of CBP and EP300 interaction with kinase inhibitors
Authors: Schonbrunn, E. / Bikowitz, M.
History
DepositionMar 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase
B: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6746
Polymers27,6962
Non-polymers1,9784
Water5,098283
1
A: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8373
Polymers13,8481
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8373
Polymers13,8481
Non-polymers9892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.080, 59.490, 57.470
Angle α, β, γ (deg.)90.000, 109.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone acetyltransferase


Mass: 13847.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP / Production host: Escherichia coli (E. coli) / References: UniProt: I3L466, histone acetyltransferase
#2: Chemical ChemComp-N6I / (3M)-4-{[(2S)-2-(3-chlorophenyl)-2-hydroxyethyl]amino}-3-[4-methyl-6-(morpholin-4-yl)-1H-benzimidazol-2-yl]pyridin-2(1H)-one


Mass: 479.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H26ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-2LO / 2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole


Mass: 509.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H33ClN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M DL-Glutamic acid monohydrate; 0.1 M DL-Alanine; 0.1 M Glycine; 0.1 M DL-Lysine monohydrochloride; 0.1 M DL-Serine, 0.1 M Imidazole, 0.1 M MES monohydrate (pH 6.5), 12 % (v/v) Ethylene ...Details: 0.1 M DL-Glutamic acid monohydrate; 0.1 M DL-Alanine; 0.1 M Glycine; 0.1 M DL-Lysine monohydrochloride; 0.1 M DL-Serine, 0.1 M Imidazole, 0.1 M MES monohydrate (pH 6.5), 12 % (v/v) Ethylene glycol, 6% w/v PEG 8000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.5→40.54 Å / Num. obs: 43721 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rrim(I) all: 0.132 / Net I/σ(I): 11.9
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3213 / CC1/2: 0.865 / Rrim(I) all: 0.818

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KPY

7kpy


Resolution: 1.5→40.54 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1811 1747 4 %
Rwork0.1604 41964 -
obs0.1613 43711 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.31 Å2 / Biso mean: 20.4804 Å2 / Biso min: 9.48 Å2
Refinement stepCycle: final / Resolution: 1.5→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 203 283 2421
Biso mean--26.98 29.28 -
Num. residues----231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.26681430.26993458360199
1.54-1.590.21221460.214635043650100
1.59-1.650.20171440.182434543598100
1.65-1.720.21450.170834733618100
1.72-1.80.1771460.167635073653100
1.8-1.890.17931440.174134613605100
1.89-2.010.20931460.159134943640100
2.01-2.160.17231460.14835123658100
2.16-2.380.16511460.137835063652100
2.38-2.720.15981460.144434953641100
2.73-3.430.17721460.15935073653100
3.43-40.540.1791490.15735933742100
Refinement TLS params.Method: refined / Origin x: -16.3893 Å / Origin y: 14.4327 Å / Origin z: -20.5116 Å
111213212223313233
T0.1193 Å2-0.0053 Å20.0089 Å2-0.094 Å2-0.0042 Å2--0.1373 Å2
L1.092 °2-0.0552 °20.3968 °2-0.2164 °2-0.0762 °2--0.6412 °2
S0.0265 Å °-0.011 Å °-0.0308 Å °0.0003 Å °-0.0099 Å °0.0066 Å °-0.005 Å °-0.0088 Å °-0.0152 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1082 - 1197
2X-RAY DIFFRACTION1allB1083 - 1197
3X-RAY DIFFRACTION1allI1 - 2
4X-RAY DIFFRACTION1allL1 - 2
5X-RAY DIFFRACTION1allQ1 - 286

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