1q3s

Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)

Method: X-RAY DIFFRACTION

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

Thermosome alpha subunit

Thermococcus sp.

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 16	MAGNESIUM ION × 14 ADENOSINE-5'-DIPHOSPHATE × 16	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	THSA_PYRKOX
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–548； UniProt 1–548 作者链 B； PDB构建体 1–548； UniProt 1–548 作者链 C； PDB构建体 1–548； UniProt 1–548 作者链 D； PDB构建体 1–548； UniProt 1–548 作者链 E； PDB构建体 1–548； UniProt 1–548 作者链 F； PDB构建体 1–548； UniProt 1–548 作者链 G； PDB构建体 1–548； UniProt 1–548 作者链 H； PDB构建体 1–548； UniProt 1–548

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	1q3s
沉积日期 deposition_date	2003-07-31
结构标题 title	Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)
关键词 keywords	chaperone, chaperonin, thermosome; CHAPERONE
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。

1q3s__assembly_1__model_1

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

下载该曲线 .dat

1q3s__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

1q3s__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	66.65 Å
Rg（电子密度）	65.55 Å
总 Rg	65.66 Å
原子数	63502
残基数	8272
排除体积	1144100 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	`1q3s__assembly_1__model_1`	hexadecameric （16）	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 (3)

实体 1 Entity 1 polymer

描述 description	Thermosome alpha subunit
分子量 formula_weight	59296.6 kDa
EC 编号 ec_number	3.6.4.9
突变 mutation	G65C
来源方法 src_method	man
拷贝数 entity_count	8

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
原子数 atom_count	31751

MAQLSGQPVVILPEGTQRYVGRDAQRLNILAARIIAETVRTTLGPKGMDKMLVDSLGDIVVTNDCATILDKIDLQHPAAKMMVEVAKTQDKEAGDGTTTAVVIAGELLRKAEELLDQNIHPSIIIKGYALAAEKAQEILDEIAIRVDPDDEETLLKIAATSITGKNAESHKELLAKLAVEAVKQVAEKKDGKYVVDLDNIKFEKKAGEGVEESELVRGVVIDKEVVHPRMPKRVENAKIALINEALEVKKTETDAKINITSPDQLMSFLEQEEKMLKDMVDHIAQTGANVVFVQKGIDDLAQHYLAKYGIMAVRRVKKSDMEKLAKATGAKIVTNVKDLTPEDLGYAEVVEERKLAGENMIFVEGCKNPKAVTILIRGGTEHVIDEVERALEDAVKVVKDVMEDGAVLPAGGAPEIELAIRLDEYAKQVGGKEALAIENFADALKIIPKTLAENAGLDTVEMLVKVISEHKNRGLGIGIDVFEGKPADMLEKGIIEPLRVKKQAIKSASEAAIMILRIDDVIAAKATKPEGGQGGGMPGGMGGMDMGM

来源 Source

来源生物 organism	Thermococcus sp.
NCBI 分类编号 ncbi_taxonomy_id	79679
宿主生物 host_organism	Escherichia coli BL21(DE3)

实体 2 Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

实体 3 Entity 3 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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6. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

结构域编号 domain_id	d1q3sa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.129 — GroEL equatorial domain-like
超家族 Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
家族 Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

结构域编号 domain_id	d1q3sa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1q3sa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.56 — GroEL-intermediate domain like
超家族 Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
家族 Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

结构域编号 domain_id	d1q3sb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.129 — GroEL equatorial domain-like
超家族 Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
家族 Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

结构域编号 domain_id	d1q3sb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1q3sb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.56 — GroEL-intermediate domain like
超家族 Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
家族 Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

结构域编号 domain_id	d1q3sc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.129 — GroEL equatorial domain-like
超家族 Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
家族 Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

结构域编号 domain_id	d1q3sc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1q3sc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.56 — GroEL-intermediate domain like
超家族 Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
家族 Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

结构域编号 domain_id	d1q3sd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.129 — GroEL equatorial domain-like
超家族 Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
家族 Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

结构域编号 domain_id	d1q3sd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1q3sd3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.56 — GroEL-intermediate domain like
超家族 Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
家族 Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

结构域编号 domain_id	d1q3se1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.129 — GroEL equatorial domain-like
超家族 Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
家族 Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

结构域编号 domain_id	d1q3se2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1q3se3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.56 — GroEL-intermediate domain like
超家族 Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
家族 Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

结构域编号 domain_id	d1q3sf1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.129 — GroEL equatorial domain-like
超家族 Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
家族 Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

结构域编号 domain_id	d1q3sf2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1q3sf3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.56 — GroEL-intermediate domain like
超家族 Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
家族 Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

结构域编号 domain_id	d1q3sg1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.129 — GroEL equatorial domain-like
超家族 Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
家族 Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

结构域编号 domain_id	d1q3sg2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1q3sg3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.56 — GroEL-intermediate domain like
超家族 Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
家族 Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

结构域编号 domain_id	d1q3sh1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.129 — GroEL equatorial domain-like
超家族 Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
家族 Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

结构域编号 domain_id	d1q3sh2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1q3sh3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.56 — GroEL-intermediate domain like
超家族 Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
家族 Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

CATH v4.4 (24 domains)

结构域编号 domain_id	1q3sA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	1q3sA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	1q3sA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	1q3sB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	1q3sB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	1q3sB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	1q3sC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	1q3sC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	1q3sC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	1q3sD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	1q3sD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	1q3sD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	1q3sE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	1q3sE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	1q3sE03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	1q3sF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	1q3sF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	1q3sF03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	1q3sG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	1q3sG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	1q3sG03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	1q3sH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	1q3sH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	1q3sH03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

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晶胞边长 a length_a	207.425 Å
晶胞边长 b length_b	236.230 Å
晶胞边长 c length_c	234.106 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	64

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	73.620 Å
R 因子 r_factor	0.2510
R_work r_work	0.2510
R_free r_free	0.2880

Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)

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

Thermosome alpha subunit

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

1q3s__assembly_1__model_1

1q3s__assembly_1__model_1 | I(q)

1q3s__assembly_1__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 (3)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. 引用文献 (2)

Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)

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

Thermosome alpha subunit

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

1q3s__assembly_1__model_1

1q3s__assembly_1__model_1 | I(q)

1q3s__assembly_1__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 (3)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. 引用文献 (2)