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Open data
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Basic information
Entry | Database: PDB / ID: 1m1d | ||||||
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Title | TETRAHYMENA GCN5 WITH BOUND BISUBSTRATE ANALOG INHIBITOR | ||||||
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![]() | TRANSFERASE / Histone Acetyltransferase / Gcn5-related N-acetyltransferase / inhibitor complex / transcription factor | ||||||
Function / homology | ![]() chromatin organization => GO:0006325 / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / histone H3 acetyltransferase activity / replication fork protection complex ...chromatin organization => GO:0006325 / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / histone H3 acetyltransferase activity / replication fork protection complex / Oxidative Stress Induced Senescence / ATAC complex / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / CENP-A containing nucleosome / histone acetyltransferase / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Poux, A.N. / Cebrat, M. / Kim, C.M. / Cole, P.A. / Marmorstein, R. | ||||||
![]() | ![]() Title: Structure of the GCN5 histone acetyltransferase bound to a bisubstrate inhibitor. Authors: Poux, A.N. / Cebrat, M. / Kim, C.M. / Cole, P.A. / Marmorstein, R. | ||||||
History |
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Remark 600 | HETEROGEN INHIBITOR COMPOSED OF A HISTONE H3 FRAGMENT (RESIDUES 1-20) AND A COENZYME A MOLECULE ...HETEROGEN INHIBITOR COMPOSED OF A HISTONE H3 FRAGMENT (RESIDUES 1-20) AND A COENZYME A MOLECULE COVALENTLY BOUND THROUGH AN ISOPROPIONYL LINKER TO LYS14. | ||||||
Remark 999 | SEQUENCE Residue 90 (Chain A) and residue 390 (Chain C) are both PHE. Author indicates that PHE is ...SEQUENCE Residue 90 (Chain A) and residue 390 (Chain C) are both PHE. Author indicates that PHE is present in many of the GCN5 homologues at that position. According to the author, residue 210 (Chain A) and residue 510 (Chain C) are both ARG and not ASN. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.9 KB | Display | ![]() |
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PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 390.9 KB | Display | ![]() |
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Full document | ![]() | 409.3 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qsnS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19457.658 Da / Num. of mol.: 2 / Fragment: Catalytic Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: GenBank: 1245146, UniProt: Q27198*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Protein/peptide | Mass: 3011.146 Da / Num. of mol.: 2 Fragment: 20 MER PEPTIDE (RESIDUES 1-20), Bisubstrate analog Source method: obtained synthetically Details: Inhibitor composed of a histone H3 fragment (residues 1-20) is chemically synthesized. The peptide's sequence occurs naturally in Saccharomyces cerevisiae (Baker's yeast). References: UniProt: P02303, UniProt: P61830*PLUS #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.09 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: Ammonium sulfate, sodium cacodylate, sodium chloride, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Feb 22, 2001 |
Radiation | Monochromator: Rosenbaum-Rock / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0082 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 27647 / Num. obs: 26519 / % possible obs: 96.1 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 97.7 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 37.3 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 97.7 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QSN Resolution: 2.2→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refinement | *PLUS Lowest resolution: 37.3 Å / % reflection Rfree: 10 % / Rfactor all: 0.271 / Rfactor obs: 0.26 / Rfactor Rfree: 0.2652 / Rfactor Rwork: 0.2134 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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