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- PDB-4tyl: Fragment-Based Screening of the Bromodomain of ATAD2 -

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Basic information

Entry
Database: PDB / ID: 4tyl
TitleFragment-Based Screening of the Bromodomain of ATAD2
ComponentsATPase family AAA domain-containing protein 2
KeywordsHydrolase/Hydrolase inhibitor / Bromodomain / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Chem-39O / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsHarner, M.J. / Chauder, B.A. / Phan, J. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)DP1OD006933/DP1CA174419 United States
CitationJournal: J.Med.Chem. / Year: 2014
Title: Fragment-Based Screening of the Bromodomain of ATAD2.
Authors: Harner, M.J. / Chauder, B.A. / Phan, J. / Fesik, S.W.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.label_alt_id_2 / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATPase family AAA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8837
Polymers15,4541
Non-polymers4296
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.492, 79.492, 137.508
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1205-

CL

21A-1346-

HOH

31A-1395-

HOH

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Components

#1: Protein ATPase family AAA domain-containing protein 2 / AAA nuclear coregulator cancer-associated protein / ANCCA


Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: UNP residues 981-1108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: Q6PL18, EC: 3.6.1.3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-39O / 5-amino-1,3,6-trimethyl-1,3-dihydro-2H-benzimidazol-2-one


Mass: 191.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N3O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 4.06 Å3/Da / Density % sol: 69.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 2.5 M (NH4)2SO4. Ligand-free crystals grown at 277K, then soaked with ligand at 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→38.183 Å / Num. obs: 22647 / % possible obs: 99.9 % / Redundancy: 23.4 % / Rmerge(I) obs: 0.063 / Rsym value: 0.083 / Net I/av σ(I): 20.37 / Net I/σ(I): 20.37
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 23.1 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.61 / % possible all: 99.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 1.85→38.183 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 2000 8.84 %
Rwork0.1605 --
obs0.1637 22634 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→38.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 0 23 251 1338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181125
X-RAY DIFFRACTIONf_angle_d1.4941530
X-RAY DIFFRACTIONf_dihedral_angle_d12.29431
X-RAY DIFFRACTIONf_chiral_restr0.084173
X-RAY DIFFRACTIONf_plane_restr0.008198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89580.28781380.23871426X-RAY DIFFRACTION99
1.8958-1.9470.231400.21444X-RAY DIFFRACTION100
1.947-2.00430.25041390.19071434X-RAY DIFFRACTION100
2.0043-2.0690.19171390.17311443X-RAY DIFFRACTION100
2.069-2.1430.18751410.16341448X-RAY DIFFRACTION100
2.143-2.22880.20921400.16221440X-RAY DIFFRACTION100
2.2288-2.33020.21021420.15781475X-RAY DIFFRACTION100
2.3302-2.4530.21781400.16731445X-RAY DIFFRACTION100
2.453-2.60670.2021420.17231466X-RAY DIFFRACTION100
2.6067-2.80790.22131430.16971475X-RAY DIFFRACTION100
2.8079-3.09030.19541440.17411481X-RAY DIFFRACTION100
3.0903-3.53720.18861460.15071502X-RAY DIFFRACTION100
3.5372-4.45540.14081470.12331518X-RAY DIFFRACTION100
4.4554-38.19110.21971590.16681637X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2184-0.22660.26481.8631-0.59152.9055-0.1521-0.05230.2448-0.05220.06-0.2635-0.160.41580.1130.1677-0.02770.01280.1715-0.00920.176635.6869-24.9951-6.0805
24.19841.29120.0481.38910.20622.69510.22280.32420.8253-0.11340.27440.3001-0.3339-1.1496-0.41090.20020.03290.01170.43170.0680.320415.3842-26.4441-0.6928
32.32010.236-0.68122.1759-0.1343.67330.4452-0.81370.91890.3482-0.07360.1505-0.9737-0.2243-0.36670.40020.03470.09740.5042-0.13370.454818.9789-19.635313.9725
42.6307-0.1751-0.46812.4937-0.17932.238-0.0242-0.25380.24260.17450.1157-0.2051-0.40980.1998-0.10610.2053-0.02020.01730.2223-0.06240.242132.9008-21.07832.257
53.79780.649-2.73891.5244-0.09923.15540.0427-0.9709-0.07690.1003-0.1071-0.19420.01050.47630.06570.1599-0.0084-0.01940.38350.00050.207126.1859-30.02628.7498
64.61783.484-0.05252.95040.27570.31240.0321-0.36990.16110.44750.34830.55520.04220.1614-0.22330.2536-0.01010.00830.54060.00180.28268.147-34.341216.1129
75.02550.0198-2.30560.8303-0.22241.7847-0.1815-0.4047-0.1542-0.00620.024-0.05890.2335-0.03580.19380.1752-0.0175-0.00650.28030.01010.21319.147-34.96722.6708
87.2129-0.77422.03153.6623-0.38566.9769-0.084-1.0322-0.19060.420.1290.0023-0.12590.2114-0.0840.19450.02170.01780.3906-0.00830.264243.962-33.4731-0.8296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 979 through 1001 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1002 through 1009 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1010 through 1030 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1031 through 1045 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1046 through 1063 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1064 through 1068 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1069 through 1092 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1093 through 1108 )

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