5U5T

Crystal structure of EED in complex with H3K27Me3 peptide and 3-(benzo[d][1,3]dioxol-4-ylmethyl)piperidine-1-carboximidamide

> 概要

5U5T の概要

関連するPDBエントリー5U5H 5U5K 5U62
分子名称Polycomb protein EED, Histone-lysine N-methyltransferase EZH2, (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide, ... (5 entities in total)
機能のキーワードeed, fragment-based generation, oncology, transcription-transferase complex, transcription/transferase
由来する生物種Homo sapiens (Human)
細胞内の位置Nucleus O75530 Q15910
ポリマー鎖数4
分子量合計92915.63
構造登録者
Bussiere, D.,Shu, W. (登録日: 2016-12-07, 公開日: 2017-01-11, 最終更新日: 2017-01-25)
主引用文献
Lingel, A.,Sendzik, M.,Huang, Y.,Shultz, M.D.,Cantwell, J.,Dillon, M.P.,Fu, X.,Fuller, J.,Gabriel, T.,Gu, J.,Jiang, X.,Li, L.,Liang, F.,McKenna, M.,Qi, W.,Rao, W.,Sheng, X.,Shu, W.,Sutton, J.,Taft, B.,Wang, L.,Zeng, J.,Zhang, H.,Zhang, M.,Zhao, K.,Lindvall, M.,Bussiere, D.E.
Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase.
J. Med. Chem., 60:415-427, 2017
PubMed: 27992714 (主引用文献が同じPDBエントリー)
DOI: 10.1021/acs.jmedchem.6b01473
MImport into Mendeley
実験手法
X-RAY DIFFRACTION (1.6 Å)
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構造検証レポート

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.206201.2%1.7%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 5u5t
回転なし
Molmil generated image of 5u5t
x軸(左右方向)周りに90°回転
Molmil generated image of 5u5t
y軸(上下方向)周りに90°回転

他の静止画像(生物学的単位)

Molmil generated image of 5u5t
回転なし
Molmil generated image of 5u5t
x軸(左右方向)周りに90°回転
Molmil generated image of 5u5t
y軸(上下方向)周りに90°回転
(*)表面構造(coarse surface)で表現されている場合、非対称単位は、赤色のリボンモデルで表示されています。
生物学的単位の座標ファイル (5u5t.pdb1.gz [138.78 KB])
生物学的単位の座標ファイル (5u5t.pdb2.gz [139.51 KB])

> 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
A, BPolycomb protein EEDpolymer36742356.22
UniProt (O75530)
Pfam (PF00400)
Homo sapiens (Human)hEED,WD protein associating with integrin cytoplasmic tails 1,WAIT-1
C, DHistone-lysine N-methyltransferase EZH2polymer303751.32
UniProt (Q15910)
Pfam (PF11616)
Homo sapiensENX-1,Enhancer of zeste homolog 2,Lysine N-methyltransferase 6
(3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamidenon-polymer261.32
YTTRIUM (III) IONnon-polymer88.92
waterwater18.01033

配列ビューア

非対称単位の内容

ポリマー鎖の数4
分子量合計92215.2
非ポリマー*分子数4
分子量合計700.5
全て*分子量合計92915.6
*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 (1.6 Å)

格子定数 [Å]92.810177.90950.340
格子定数 [度]90.0090.0090.00
空間群P 21 21 2
分解能 [Å] (低 - 高)64.22 - 1.60
最も高い分解能シェルの値1.640 - 1.600
R因子0.17
R-work0.16800
最も高い分解能シェルの値0.225
R-free0.20000
最も高い分解能シェルの値0.248
結合長の平均二乗偏差(RMSD) [Å]0.010
結合角の平均二乗偏差(RMSD) [度]1.060

回折データの統計情報

分解能 [Å] (低 - 高)82.29 - 1.60
最も高い分解能シェルの値 -
独立反射数110710
完全性 [%]97.2
冗長性5.8

結晶化条件

結晶ID方法pHpHの範囲温度単位
1VAPOR DIFFUSION, HANGING DROP291

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
A0005829cellular_componentcytosol
A0035098cellular_componentESC/E(Z) complex
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0045120cellular_componentpronucleus
A0001739cellular_componentsex chromatin
A0003682molecular_functionchromatin binding
A0042054molecular_functionhistone methyltransferase activity
A0042802molecular_functionidentical protein binding
A0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
A0070734biological_processhistone H3-K27 methylation
A0045814biological_processnegative regulation of gene expression, epigenetic
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0045892biological_processnegative regulation of transcription, DNA-templated
A0061087biological_processpositive regulation of histone H3-K27 methylation
A2000011biological_processregulation of adaxial/abaxial pattern formation
A0006349biological_processregulation of gene expression by genetic imprinting
A0021510biological_processspinal cord development
A0006351biological_processtranscription, DNA-templated
B0005829cellular_componentcytosol
B0035098cellular_componentESC/E(Z) complex
B0005654cellular_componentnucleoplasm
B0005634cellular_componentnucleus
B0045120cellular_componentpronucleus
B0001739cellular_componentsex chromatin
B0003682molecular_functionchromatin binding
B0042054molecular_functionhistone methyltransferase activity
B0042802molecular_functionidentical protein binding
B0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
B0070734biological_processhistone H3-K27 methylation
B0045814biological_processnegative regulation of gene expression, epigenetic
B0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
B0045892biological_processnegative regulation of transcription, DNA-templated
B0061087biological_processpositive regulation of histone H3-K27 methylation
B2000011biological_processregulation of adaxial/abaxial pattern formation
B0006349biological_processregulation of gene expression by genetic imprinting
B0021510biological_processspinal cord development
B0006351biological_processtranscription, DNA-templated
C0005737cellular_componentcytoplasm
C0035098cellular_componentESC/E(Z) complex
C0000790cellular_componentnuclear chromatin
C0005654cellular_componentnucleoplasm
C0005634cellular_componentnucleus
C0045120cellular_componentpronucleus
C0003682molecular_functionchromatin binding
C0031490molecular_functionchromatin DNA binding
C0001047molecular_functioncore promoter binding
C0003677molecular_functionDNA binding
C0042054molecular_functionhistone methyltransferase activity
C0046976molecular_functionhistone methyltransferase activity (H3-K27 specific)
C0018024molecular_functionhistone-lysine N-methyltransferase activity
C0070878molecular_functionprimary miRNA binding
C1990841molecular_functionpromoter-specific chromatin binding
C0016279molecular_functionprotein-lysine N-methyltransferase activity
C0043021molecular_functionribonucleoprotein complex binding
C0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
C0014898biological_processcardiac muscle hypertrophy in response to stress
C0070301biological_processcellular response to hydrogen peroxide
C0035984biological_processcellular response to trichostatin A
C0021695biological_processcerebellar cortex development
C0006325biological_processchromatin organization
C0006306biological_processDNA methylation
C0070314biological_processG1 to G0 transition
C0036333biological_processhepatocyte homeostasis
C0021766biological_processhippocampus development
C0070734biological_processhistone H3-K27 methylation
C0098532biological_processhistone H3-K27 trimethylation
C0016571biological_processhistone methylation
C0097421biological_processliver regeneration
C0045605biological_processnegative regulation of epidermal cell differentiation
C2000134biological_processnegative regulation of G1/S transition of mitotic cell cycle
C0045814biological_processnegative regulation of gene expression, epigenetic
C0048387biological_processnegative regulation of retinoic acid receptor signaling pathway
C0043433biological_processnegative regulation of sequence-specific DNA binding transcription factor activity
C0051154biological_processnegative regulation of striated muscle cell differentiation
C0034244biological_processnegative regulation of transcription elongation from RNA polymerase II promoter
C0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
C0045892biological_processnegative regulation of transcription, DNA-templated
C1900006biological_processpositive regulation of dendrite development
C0010718biological_processpositive regulation of epithelial to mesenchymal transition
C0043547biological_processpositive regulation of GTPase activity
C0043406biological_processpositive regulation of MAP kinase activity
C0071902biological_processpositive regulation of protein serine/threonine kinase activity
C0071168biological_processprotein localization to chromatin
C0042127biological_processregulation of cell proliferation
C0042752biological_processregulation of circadian rhythm
C0014013biological_processregulation of gliogenesis
C0006355biological_processregulation of transcription, DNA-templated
C0032355biological_processresponse to estradiol
C1904772biological_processresponse to tetrachloromethane
C0048511biological_processrhythmic process
C0014834biological_processskeletal muscle satellite cell maintenance involved in skeletal muscle regeneration
C0006351biological_processtranscription, DNA-templated
D0005737cellular_componentcytoplasm
D0035098cellular_componentESC/E(Z) complex
D0000790cellular_componentnuclear chromatin
D0005654cellular_componentnucleoplasm
D0005634cellular_componentnucleus
D0045120cellular_componentpronucleus
D0003682molecular_functionchromatin binding
D0031490molecular_functionchromatin DNA binding
D0001047molecular_functioncore promoter binding
D0003677molecular_functionDNA binding
D0042054molecular_functionhistone methyltransferase activity
D0046976molecular_functionhistone methyltransferase activity (H3-K27 specific)
D0018024molecular_functionhistone-lysine N-methyltransferase activity
D0070878molecular_functionprimary miRNA binding
D1990841molecular_functionpromoter-specific chromatin binding
D0016279molecular_functionprotein-lysine N-methyltransferase activity
D0043021molecular_functionribonucleoprotein complex binding
D0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
D0014898biological_processcardiac muscle hypertrophy in response to stress
D0070301biological_processcellular response to hydrogen peroxide
D0035984biological_processcellular response to trichostatin A
D0021695biological_processcerebellar cortex development
D0006325biological_processchromatin organization
D0006306biological_processDNA methylation
D0070314biological_processG1 to G0 transition
D0036333biological_processhepatocyte homeostasis
D0021766biological_processhippocampus development
D0070734biological_processhistone H3-K27 methylation
D0098532biological_processhistone H3-K27 trimethylation
D0016571biological_processhistone methylation
D0097421biological_processliver regeneration
D0045605biological_processnegative regulation of epidermal cell differentiation
D2000134biological_processnegative regulation of G1/S transition of mitotic cell cycle
D0045814biological_processnegative regulation of gene expression, epigenetic
D0048387biological_processnegative regulation of retinoic acid receptor signaling pathway
D0043433biological_processnegative regulation of sequence-specific DNA binding transcription factor activity
D0051154biological_processnegative regulation of striated muscle cell differentiation
D0034244biological_processnegative regulation of transcription elongation from RNA polymerase II promoter
D0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
D0045892biological_processnegative regulation of transcription, DNA-templated
D1900006biological_processpositive regulation of dendrite development
D0010718biological_processpositive regulation of epithelial to mesenchymal transition
D0043547biological_processpositive regulation of GTPase activity
D0043406biological_processpositive regulation of MAP kinase activity
D0071902biological_processpositive regulation of protein serine/threonine kinase activity
D0071168biological_processprotein localization to chromatin
D0042127biological_processregulation of cell proliferation
D0042752biological_processregulation of circadian rhythm
D0014013biological_processregulation of gliogenesis
D0006355biological_processregulation of transcription, DNA-templated
D0032355biological_processresponse to estradiol
D1904772biological_processresponse to tetrachloromethane
D0048511biological_processrhythmic process
D0014834biological_processskeletal muscle satellite cell maintenance involved in skeletal muscle regeneration
D0006351biological_processtranscription, DNA-templated
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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
AC112binding site for residue 7W7 A 501
鎖名残基
APHE97
ATYR148
AASN194
AGLU238
AASP310
ATYR365
AMET366
AARG367
AARG414
AHOH612
AHOH692
AHOH731

AC23binding site for residue YT3 B 501
鎖名残基
BARG269
BLYS293
BHIS295

AC32binding site for residue YT3 B 502
鎖名残基
AARG269
ALYS293

AC411binding site for residue 7W7 B 503
鎖名残基
BPHE97
BTYR148
BASN194
BGLU238
BASP310
BTYR365
BMET366
BARG367
BARG414
BHOH673
BHOH742

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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
7W7_5u5t_A_50111(3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide binding site
鎖名残基ligand
APHE977W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
ATYR1487W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
AASN1947W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
AGLU2387W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
ALEU2407W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
AMET2567W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
AASP3107W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
ATYR365-ARG3677W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
AARG4147W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide

7W7_5u5t_B_50310(3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide binding site
鎖名残基ligand
BPHE977W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
BTYR1487W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
BASN1947W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
BGLU2387W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
BLEU2407W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
BASP3107W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
BTYR365-ARG3677W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide
BARG4147W7: (3R)-3-[(2H-1,3-benzodioxol-4-yl)methyl]piperidine-1-carboximidamide

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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
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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
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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

> 相同蛋白質

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Resources

ファイル形式ファイル名 (ファイルサイズ)
PDB全ての情報pdb5u5t.ent.gz (280.82 KB)
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全ての情報 (非圧縮)pdb5u5t.ent (1.08 MB)
ヘッダのみpdb5u5t.ent.gz (9.18 KB)
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PDBx/mmCIF5u5t.cif.gz (340.63 KB)
PDBML
全ての情報5u5t.xml.gz (464.54 KB)
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ヘッダのみ5u5t-noatom.xml.gz (41.23 KB)
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座標情報のみ5u5t-extatom.xml.gz (161.76 KB)
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PDBMLplus全ての情報5u5t-plus.xml.gz (468.71 KB)
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ヘッダのみ5u5t-plus-noatom.xml.gz (45.41 KB)
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付加情報のみ5u5t-add.xml.gz (4.17 KB)
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RDF5u5t.rdf.gz (86.89 KB)
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構造因子r5u5tsf.ent.gz (3.69 MB)
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生物学的単位 (PDB形式)5u5t.pdb1.gz (138.78 KB) (A,C)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5u5t.pdb2.gz (139.51 KB) (B,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
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検証レポートPDF5u5t​_validation.pdf.gz (450.76 KB)
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PDF-full5u5t​_full​_validation.pdf.gz (452.96 KB)
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XML5u5t​_validation.xml.gz (37.71 KB)
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PNG5u5t​_multipercentile​_validation.png.gz (135.12 KB)
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SVG5u5t​_multipercentile​_validation.svg.gz (926 B)
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Sequence (fasta)5u5t​_seq.txt
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