3fbv

Crystal structure of the oligomer formed by the kinase-ribonuclease domain of Ire1

Method: X-RAY DIFFRACTION

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Serine/threonine-protein kinase/endoribonuclease IRE1

Saccharomyces cerevisiae

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白同源多聚体	同源多聚体	蛋白 14	N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 14	与蛋白数一致
2	蛋白同源多聚体	同源多聚体	蛋白 2	N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 2	与蛋白数一致
3	蛋白同源多聚体	同源多聚体	蛋白 2	N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 2	与蛋白数一致
4	蛋白同源多聚体	同源多聚体	蛋白 2	N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 2	与蛋白数一致
5	蛋白同源多聚体	同源多聚体	蛋白 2	N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 2	与蛋白数一致
6	蛋白同源多聚体	同源多聚体	蛋白 2	N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 2	与蛋白数一致
7	蛋白同源多聚体	同源多聚体	蛋白 2	N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 2	与蛋白数一致
8	蛋白同源多聚体	同源多聚体	蛋白 2	N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 2	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	IRE1_YEAST
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 2–448； UniProt 641–1115 作者链 B； PDB构建体 2–448； UniProt 641–1115 作者链 C； PDB构建体 2–448； UniProt 641–1115 作者链 D； PDB构建体 2–448； UniProt 641–1115 作者链 E； PDB构建体 2–448； UniProt 641–1115 作者链 F； PDB构建体 2–448； UniProt 641–1115 作者链 G； PDB构建体 2–448； UniProt 641–1115 作者链 H； PDB构建体 2–448； UniProt 641–1115 作者链 I； PDB构建体 2–448； UniProt 641–1115 作者链 J； PDB构建体 2–448； UniProt 641–1115 作者链 K； PDB构建体 2–448； UniProt 641–1115 作者链 L； PDB构建体 2–448； UniProt 641–1115 作者链 M； PDB构建体 2–448； UniProt 641–1115 作者链 N； PDB构建体 2–448； UniProt 641–1115

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3fbv
沉积日期 deposition_date	2008-11-19
结构标题 title	Crystal structure of the oligomer formed by the kinase-ribonuclease domain of Ire1
关键词 keywords	;IRE1, RNase, ribonuclease, complex, kinase, inhibitor, oligomer, cytoplasmic, APY29, aminopyrazole, ATP-binding, Endoplasmic reticulum, Glycoprotein, Hydrolase, Magnesium, Membrane, Metal-binding, Multifunctional enzyme, Nucleotide-binding, Phosphoprotein, Serine/threonine-protein kinase, Transcription, Transcription regulation, Transferase, Transmembrane, Unfolded protein response ;; TRANSFERASE, HYDROLASE
实验方法 method	X-RAY DIFFRACTION

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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

3fbv__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

3fbv__assembly_3__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

3fbv__assembly_3__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	30.95 Å
Rg（电子密度）	29.87 Å
总 Rg	30.64 Å
原子数	6906
残基数	837
排除体积	123430 Å³
最大 q	0.500 Å⁻¹

Assembly	Model	结构单元	聚集说明	状态	CRYSOL	操作
1	1	`3fbv__assembly_1__model_1`	tetradecameric （14）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`3fbv__assembly_2__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
3	1	`3fbv__assembly_3__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
4	1	`3fbv__assembly_4__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
5	1	`3fbv__assembly_5__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
6	1	`3fbv__assembly_6__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
7	1	`3fbv__assembly_7__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
8	1	`3fbv__assembly_8__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合物信息 Entities & Polymers (2)

实体 1 Entity 1 polymer

描述 description	Serine/threonine-protein kinase/endoribonuclease IRE1
分子量 formula_weight	51883.4 kDa
EC 编号 ec_number	2.7.11.1, 3.1.26.-
突变 mutation	Amino acids 865-892 deleted
来源方法 src_method	man
拷贝数 entity_count	14

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
原子数 atom_count	48018

PEKKKRKRGSRGGKKGRKSRIANIPNFEQSLKNLVVSEKILGYGSSGTVVFQGSFQGRPVAVKRMLIDFCDIALMEIKLLTESDDHPNVIRYYCSETTDRFLYIALELCNLNLQDLVESKNVSDENLKLQKEYNPISLLRQIASGVAHLHSLKIIHRDLKPQNILVSTSSRFTADQQTGAENLRILISDFGLCKKLDSGQSSFRTNLNNPSGTSGWRAPELLEESTKRRLTRSIDIFSMGCVFYYILSKGKHPFGDKYSRESNIIRGIFSLDEMKCLHDRSLIAEATDLISQMIDHDPLKRPTAMKVLRHPLFWPKSKKLEFLLKVSDRLEIENRDPPSALLMKFDAGSDFVIPSGDWTVKFDKTFMDNLERYRKYHSSKLMDLLRALRNKYHHFMDLPEDIAELMGPVPDGFYDYFTKRFPNLLIGVYMIVKENLSDDQILREFLYS

来源 Source

来源生物 organism	Saccharomyces cerevisiae
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	N~2~-1H-benzimidazol-5-yl-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine
分子量 formula_weight	332.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	14

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6. 折叠分类 (SCOP + CATH) 42 domains

CATH v4.4 (42 domains)

结构域编号 domain_id	3fbvA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvE03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvF03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvG02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvG03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvH02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvH03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvI02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvI03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvJ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvJ02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvJ03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvK02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvK03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvL02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvL03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvM01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvM02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvM03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

结构域编号 domain_id	3fbvN01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3fbvN02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3fbvN03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	180 — KEN domain

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晶胞边长 a length_a	156.820 Å
晶胞边长 b length_b	163.470 Å
晶胞边长 c length_c	292.830 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	56

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	19.983 Å
R 因子 r_factor	0.2374
R_work r_work	0.2352
R_free r_free	0.2835

Crystal structure of the oligomer formed by the kinase-ribonuclease domain of Ire1

1. 蛋白身份与相关结构 Protein Identity & Related Structures

Serine/threonine-protein kinase/endoribonuclease IRE1

当前结构中的状态

数据库中的同蛋白其他状态

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

3fbv__assembly_3__model_1

3fbv__assembly_3__model_1 | I(q)

3fbv__assembly_3__model_1 | P(r) · Pending

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合物信息 Entities & Polymers (2)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

6. 折叠分类 (SCOP + CATH) 42 domains

CATH v4.4 (42 domains)

7. 引用文献 (1)

Crystal structure of the oligomer formed by the kinase-ribonuclease domain of Ire1

1. 蛋白身份与相关结构 Protein Identity & Related Structures

Serine/threonine-protein kinase/endoribonuclease IRE1

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

3fbv__assembly_3__model_1

3fbv__assembly_3__model_1 | I(q)

3fbv__assembly_3__model_1 | P(r) · Pending

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合物信息 Entities & Polymers (2)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

6. 折叠分类 (SCOP + CATH) 42 domains

CATH v4.4 (42 domains)

7. 引用文献 (1)