3BIY

Crystal structure of p300 histone acetyltransferase domain in complex with a bisubstrate inhibitor, Lys-CoA

> Summary

Summary for 3BIY

DescriptorHistone acetyltransferase p300 (E.C.2.3.1.48)
Functional Keywordsp300 hat, bisubstrate inhibitor, protein-inhibitor complex, transferase
Biological sourceHomo sapiens (human)
Cellular locationCytoplasm Q09472
Total number of polymer chains1
Total molecular weight45370.67
Authors
Liu, X.,Wang, L.,Zhao, K.,Thompson, P.R.,Hwang, Y.,Marmorstein, R.,Cole, P.A. (deposition date: 2007-12-02, release date: 2008-02-12, modification date: 2011-07-13)
Primary citation
Liu, X.,Wang, L.,Zhao, K.,Thompson, P.R.,Hwang, Y.,Marmorstein, R.,Cole, P.A.
The structural basis of protein acetylation by the p300/CBP transcriptional coactivator
Nature, 451:846-850, 2008
PubMed: 18273021
DOI: 10.1038/nature06546
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.7 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.211602.1%8.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 3biy
no rotation
Molmil generated image of 3biy
rotated about x axis by 90°
Molmil generated image of 3biy
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AHistone acetyltransferase p300polymer38043976.41
UniProt (Q09472)
Pfam (PF00569)
Pfam (PF08214)
Homo sapiens (human)@PDBjE1A-associated protein p300
BROMIDE IONnon-polymer79.95
[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATEnon-polymer994.81
waterwater18.0234

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight43976.4
Non-Polymers*Number of molecules6
Total molecular weight1394.3
All*Total molecular weight45370.7
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.7 Å)

Cell axes61.51361.513101.153
Cell angles90.0090.0090.00
SpacegroupP 43
Resolution limits26.65 - 1.70
the highest resolution shell value1.744 - 1.700
R-factor0.18312
R-work0.18158
the highest resolution shell value0.203
R-free0.21342
the highest resolution shell value0.270
RMSD bond length0.011
RMSD bond angle1.411

Data Collection Statistics

Resolution limits50.00 - 1.70
the highest resolution shell value -
Number of reflections41358
Rmerge_l_obs0.044
the highest resolution shell value0.658
Completeness99.9
Redundancy5.6
the highest resolution shell value5.5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7.5293
1VAPOR DIFFUSION, HANGING DROP7.5293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0000785cellular_componentchromatin
A0005737cellular_componentcytoplasm
A0000123cellular_componenthistone acetyltransferase complex
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0032993cellular_componentprotein-DNA complex
A0005667cellular_componenttranscription factor complex
A0016407molecular_functionacetyltransferase activity
A0033613molecular_functionactivating transcription factor binding
A0050681molecular_functionandrogen receptor binding
A0003823molecular_functionantigen binding
A0008013molecular_functionbeta-catenin binding
A0003682molecular_functionchromatin binding
A0031490molecular_functionchromatin DNA binding
A0001047molecular_functioncore promoter binding
A0003684molecular_functiondamaged DNA binding
A0003677molecular_functionDNA binding
A0004402molecular_functionhistone acetyltransferase activity
A0004468molecular_functionlysine N-acetyltransferase activity, acting on acetyl phosphate as donor
A0035257molecular_functionnuclear hormone receptor binding
A0034212molecular_functionpeptide N-acetyltransferase activity
A0097157molecular_functionpre-mRNA intronic binding
A0008022molecular_functionprotein C-terminus binding
A0001102molecular_functionRNA polymerase II activating transcription factor binding
A0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
A0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
A0003713molecular_functiontranscription coactivator activity
A0008134molecular_functiontranscription factor binding
A0001228molecular_functiontranscriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
A0016746molecular_functiontransferase activity, transferring acyl groups
A0008270molecular_functionzinc ion binding
A0006915biological_processapoptotic process
A0030183biological_processB cell differentiation
A1904837biological_processbeta-catenin-TCF complex assembly
A0071320biological_processcellular response to cAMP
A0071549biological_processcellular response to dexamethasone stimulus
A0035690biological_processcellular response to drug
A0071333biological_processcellular response to glucose stimulus
A0070301biological_processcellular response to hydrogen peroxide
A0071389biological_processcellular response to mineralocorticoid stimulus
A1990090biological_processcellular response to nerve growth factor stimulus
A0071300biological_processcellular response to retinoic acid
A0035984biological_processcellular response to trichostatin A
A0034644biological_processcellular response to UV
A0007623biological_processcircadian rhythm
A0048565biological_processdigestive tract development
A0006977biological_processDNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
A0045444biological_processfat cell differentiation
A0007507biological_processheart development
A0043969biological_processhistone H2B acetylation
A0043966biological_processhistone H3 acetylation
A0043967biological_processhistone H4 acetylation
A0018393biological_processinternal peptidyl-lysine acetylation
A0006475biological_processinternal protein amino acid acetylation
A0042771biological_processintrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
A0001889biological_processliver development
A0030324biological_processlung development
A0035855biological_processmegakaryocyte development
A0007613biological_processmemory
A0018076biological_processN-terminal peptidyl-lysine acetylation
A0043154biological_processnegative regulation of cysteine-type endopeptidase activity involved in apoptotic process
A2000629biological_processnegative regulation of miRNA metabolic process
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0007399biological_processnervous system development
A0007219biological_processNotch signaling pathway
A0009887biological_processorgan morphogenesis
A0030220biological_processplatelet formation
A0043923biological_processpositive regulation by host of viral transcription
A0045773biological_processpositive regulation of axon extension
A0010942biological_processpositive regulation of cell death
A0045793biological_processpositive regulation of cell size
A0032967biological_processpositive regulation of collagen biosynthetic process
A0043388biological_processpositive regulation of DNA binding
A0045815biological_processpositive regulation of gene expression, epigenetic
A0010560biological_processpositive regulation of glycoprotein biosynthetic process
A0035066biological_processpositive regulation of histone acetylation
A0014737biological_processpositive regulation of muscle atrophy
A0032092biological_processpositive regulation of protein binding
A0033160biological_processpositive regulation of protein import into nucleus, translocation
A0001934biological_processpositive regulation of protein phosphorylation
A0050714biological_processpositive regulation of protein secretion
A0045862biological_processpositive regulation of proteolysis
A0060298biological_processpositive regulation of sarcomere organization
A0051091biological_processpositive regulation of sequence-specific DNA binding transcription factor activity
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0006990biological_processpositive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response
A0045727biological_processpositive regulation of translation
A0032481biological_processpositive regulation of type I interferon production
A0006473biological_processprotein acetylation
A0043491biological_processprotein kinase B signaling
A0050821biological_processprotein stabilization
A0065004biological_processprotein-DNA complex assembly
A0060765biological_processregulation of androgen receptor signaling pathway
A0060177biological_processregulation of angiotensin metabolic process
A0010506biological_processregulation of autophagy
A0051726biological_processregulation of cell cycle
A1900034biological_processregulation of cellular response to heat
A1901796biological_processregulation of signal transduction by p53 class mediator
A0061418biological_processregulation of transcription from RNA polymerase II promoter in response to hypoxia
A0006355biological_processregulation of transcription, DNA-templated
A0090043biological_processregulation of tubulin deacetylation
A0051592biological_processresponse to calcium ion
A0032025biological_processresponse to cobalt ion
A0043627biological_processresponse to estrogen
A0045471biological_processresponse to ethanol
A0070542biological_processresponse to fatty acid
A0001666biological_processresponse to hypoxia
A0034612biological_processresponse to tumor necrosis factor
A0007519biological_processskeletal muscle tissue development
A0001756biological_processsomitogenesis
A0002223biological_processstimulatory C-type lectin receptor signaling pathway
A0006283biological_processtranscription-coupled nucleotide-excision repair
A0016032biological_processviral process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14BINDING SITE FOR RESIDUE BR A 1521
ChainResidue
ALYS140
AHOH
AHOH
AHOH

AC21BINDING SITE FOR RESIDUE BR A 1522
ChainResidue
AGLN375

AC31BINDING SITE FOR RESIDUE BR A 1523
ChainResidue
AASN18

AC41BINDING SITE FOR RESIDUE BR A 1524
ChainResidue
AHOH

AC55BINDING SITE FOR RESIDUE BR A 1525
ChainResidue
APRO120
ALYS121
ASER190
AHOH
AHOH

AC631BINDING SITE FOR RESIDUE 01K A 700
ChainResidue
ASER110
ATYR111
ALEU112
AASP113
ASER114
AARG124
ATHR125
ATYR128
ATRP150
ACYS152
APRO154
ATYR160
ALYS170
AILE171
APRO172
AARG176
ATRP180
ATYR181
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH
AHOH

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
01K_3biy_A_70029[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE binding site
ChainResidueligand
AILE1395-SER140001K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
ALYS140701K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
AARG1410-THR141101K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
ATYR141401K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
AILE1435-PRO144001K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
AASP144401K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
ATYR144601K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
AHIS145101K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
AGLN1455-LYS145901K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
AARG1462-LEU146301K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
ATRP1466-TYR146701K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE
AARG162701K: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R,20R)-20-CARBAMOYL-3-HYDROXY-2,2-DIMETHYL-4,8,14,22-TETRAOXO-12-THIA-5,9,15,21-TETRAAZATRICOS-1-YL DIHYDROGEN DIPHOSPHATE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

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