5H85

Crystal structure of the bromodomain of human CREBBP in complex with UO37D

> 概要

5H85 の概要

分子名称CREB-binding protein, methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate (3 entities in total)
機能のキーワードtranscription, inhibitor, transferase
由来する生物種Homo sapiens (Human)
細胞内の位置Cytoplasm Q92793
ポリマー鎖数1
分子量合計14520.62
構造登録者
Dong, J.,Caflisch, A. (登録日: 2015-12-23, 公開日: 2017-01-11)
主引用文献
Dong, J.,Caflisch, A.
Crystal structure of the bromodomain of human CREBBP in complex with UO37D
To Be Published,
実験手法
X-RAY DIFFRACTION (1.701 Å)
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構造検証レポート

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.1682000.8%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution
検証レポート(詳細版)をダウンロード

他の静止画像(非対称単位)

Molmil generated image of 5h85
回転なし
Molmil generated image of 5h85
x軸(左右方向)周りに90°回転
Molmil generated image of 5h85
y軸(上下方向)周りに90°回転

> 構造情報

エンティティ

鎖名説明種類鎖長分子量分子数データベース名(アクセス番号)由来する生物種エンティティの一般名
ACREB-binding proteinpolymer11914223.31
UniProt (Q92793)
Pfam (PF00439)
Homo sapiens (Human)
methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoatenon-polymer297.31
waterwater18.0220

配列ビューア

非対称単位の内容

ポリマー鎖の数1
分子量合計14223.3
非ポリマー*分子数1
分子量合計297.3
全て*分子量合計14520.6
*水分子は含んでいません

> 実験情報

精密化の統計情報

実験手法:X-RAY DIFFRACTION (1.701 Å)

格子定数 [Å]24.41345.314104.660
格子定数 [度]90.0090.0090.00
空間群P 21 21 21
分解能 [Å] (低 - 高)41.58 - 1.70
最も高い分解能シェルの値1.832 - 1.701
R因子0.163
R-work0.16110
最も高い分解能シェルの値0.172
R-free0.19850
最も高い分解能シェルの値0.220
結合長の平均二乗偏差(RMSD) [Å]0.006
結合角の平均二乗偏差(RMSD) [度]0.832

回折データの統計情報

分解能 [Å] (低 - 高)52.33 - 1.70
最も高い分解能シェルの値 -
独立反射数13297
最も高い分解能シェルの値0.400
完全性 [%]98.8
冗長性11.4
最も高い分解能シェルの値9.1

結晶化条件

結晶ID方法pHpHの範囲温度単位
1VAPOR DIFFUSION, HANGING DROP7.5277

結晶化試薬

ID結晶ID濃度試薬名濃度 (単位)詳細
文献の結晶化試薬*
ID結晶ID溶液試薬名濃度 (単位) (単位)詳細
注釈情報は下記文献より抽出しています*

> 機能情報

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GO(遺伝子オントロジー)由来の情報

鎖名GO(遺伝子オントロジー)id名前空間内容
A0005737cellular_componentcytoplasm
A0000123cellular_componenthistone acetyltransferase complex
A0016604cellular_componentnuclear body
A0000790cellular_componentnuclear chromatin
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0016407molecular_functionacetyltransferase activity
A0003682molecular_functionchromatin binding
A0000987molecular_functioncore promoter proximal region sequence-specific DNA binding
A0003684molecular_functiondamaged DNA binding
A0004402molecular_functionhistone acetyltransferase activity
A0043426molecular_functionMRF binding
A0002039molecular_functionp53 binding
A0034212molecular_functionpeptide N-acetyltransferase activity
A0001102molecular_functionRNA polymerase II activating transcription factor binding
A0001105molecular_functionRNA polymerase II transcription coactivator activity
A0001085molecular_functionRNA polymerase II transcription factor binding
A0004871molecular_functionsignal transducer activity
A0003713molecular_functiontranscription coactivator activity
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0008134molecular_functiontranscription factor binding
A0001078molecular_functiontranscriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
A0001191molecular_functiontranscriptional repressor activity, RNA polymerase II transcription factor binding
A0008270molecular_functionzinc ion binding
A1904837biological_processbeta-catenin-TCF complex assembly
A0044255biological_processcellular lipid metabolic process
A0034644biological_processcellular response to UV
A0042733biological_processembryonic digit morphogenesis
A0016573biological_processhistone acetylation
A0042592biological_processhomeostatic process
A0018076biological_processN-terminal peptidyl-lysine acetylation
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0007219biological_processNotch signaling pathway
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0045893biological_processpositive regulation of transcription, DNA-templated
A0032481biological_processpositive regulation of type I interferon production
A0006473biological_processprotein acetylation
A0006461biological_processprotein complex assembly
A0042981biological_processregulation of apoptotic process
A1900034biological_processregulation of cellular response to heat
A0008589biological_processregulation of smoothened signaling pathway
A0061418biological_processregulation of transcription from RNA polymerase II promoter in response to hypoxia
A0006355biological_processregulation of transcription, DNA-templated
A0001666biological_processresponse to hypoxia
A0048511biological_processrhythmic process
A0007165biological_processsignal transduction
A0002223biological_processstimulatory C-type lectin receptor signaling pathway
A0006367biological_processtranscription initiation from RNA polymerase II promoter
A0016032biological_processviral process
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PDBデータベースに由来する情報

site_id残基数詳細
AC111binding site for residue 5XS A 1201
鎖名残基
APRO1110
AGLN1113
AVAL1115
AASN1168
AVAL1174
AHOH1317
AHOH1370
AHOH1380
AHOH1410
AHOH1429
AHOH1446

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「HETATM」原子の座標から抽出されたリガンド結合部位

site_id残基数詳細
5XS_5h85_A_120113methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate binding site
鎖名残基ligand
ALEU1109-PHE11115XS: methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate
AGLN11135XS: methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate
AVAL11155XS: methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate
ALEU11205XS: methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate
AILE11225XS: methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate
ATYR11255XS: methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate
AALA11645XS: methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate
ATYR1167-ASN11685XS: methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate
AARG1173-VAL11745XS: methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate

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UniProtにおけるモチーフ・データベースPROSITEからの機能情報

site_id残基数詳細
PS006331
鎖名残基詳細
ASER1108-TYR1167

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SwissProt/UniProtに記載されている蛋白質分子機能情報

site_id残基数詳細
SWS_FT_FI41Acetyl-CoA; via carbonyl oxygen. {ECO:0000250|UniProtKB:Q09472}.
鎖名残基詳細
ANA*

SWS_FT_FI52Acetyl-CoA. {ECO:0000250|UniProtKB:Q09472}.
鎖名残基詳細
ANA*
ANA*

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CSAにおける酵素触媒機能の情報

site_id残基数詳細

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