- PDB-5lj0: Crystal structure of human ATAD2 bromodomain in complex with 8-((... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5lj0
Title
Crystal structure of human ATAD2 bromodomain in complex with 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one
Components
ATPase family AAA domain-containing protein 2
Keywords
TRANSCRIPTION / INHIBITOR / ATAD2 / BROMODOMAIN / EPIGENETICS / ATPase family AAA domain-containing protein 2
Function / homology
Function and homology information
nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome ...nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / 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
ATPasefamilyAAAdomain-containingprotein2 / AAA nuclear coregulator cancer-associated protein / ANCCA
Mass: 15453.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SM first two residues are residual after cleavage of the expression tag Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18, EC: 3.6.1.3
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.95373 Å / Relative weight: 1
Reflection
Resolution: 1.82→135.86 Å / Num. obs: 23289 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.3
Reflection shell
Resolution: 1.82→1.92 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 5.2 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0073
refinement
XDS
datareduction
SCALA
datascaling
Refinement
Resolution: 1.82→68.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.419 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18256
1192
5.1 %
RANDOM
Rwork
0.17378
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obs
0.17424
22036
99.97 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å