2b5i

cytokine receptor complex

Method: X-RAY DIFFRACTION D_max: 101.0 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2b5i
沉积日期 deposition_date	2005-09-28
结构标题 title	cytokine receptor complex
关键词 keywords	four-helix bundle, Fibronectin domain, CYTOKINE-CYTOKINE RECEPTOR COMPLEX; CYTOKINE/CYTOKINE RECEPTOR
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	31.61 Å
回转半径 Rg (电子) rg_electron	30.69 Å
零角强度 I(0) i0	92393700.00
分子量 molecular_weight	75289.0 kDa
排除体积 excluded_volume	93880 Å³
包络体积 envelope_volume	123600 Å³
水化壳体积 shell_volume	34199 Å³
包络直径 envelope_diameter	107.1 Å
壳层 Rg shell_rg	37.04 Å
包络 Rg envelope_rg	30.93 Å
形状 Rg shape_rg	30.68 Å
总 Rg total_rg	31.30 Å
总原子数 total_atoms	5292
残基数 n_residues	629
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	101.0 Å
Rg (实空间) rg_real	31.55 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	9.2390e+07
I(0) 误差 (实空间) i0_real_error	1.4480e+06
Rg (倒空间) rg_reciprocal	31.58 Å
I(0) (倒空间) i0_reciprocal	92400000.0000
解质量估计 total_estimate	0.9017
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	42.4 Å
偏度 Skewness skewness	0.209
峰度 Kurtosis kurtosis	-0.508
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12680000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.897

▶

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

▶

5. 实体与聚合体信息 (7)

Entity 1 polymer

描述 description	Interleukin-2
分子量 formula_weight	15436.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	5463

APTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNRWITFCQSIISTLT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 2 polymer

描述 description	Interleukin-2 receptor beta chain
分子量 formula_weight	24761.1 kDa
突变 mutation	N3Q,N17Q,N45Q
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

AVQGTSQFTCFYNSRAQISCVWSQDGALQDTSCQVHAWPDRRRWQQTCELLPVSQASWACNLILGAPDSQKLTTVDIVTLRVLCREGVRWRVMAIQDFKPFENLRLMAPISLQVVHVETHRCNISWEISQASHYFERHLEFEARTLSPGHTWEEAPLLTLKQKQEWICLETLTPDTQYEFQVRVKPLQGEFTTWSPWSQPLAFRTKPAALGKDT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 3 polymer

描述 description	Cytokine receptor common gamma chain
分子量 formula_weight	23912.7 kDa
突变 mutation	N53Q
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

PLPEVQCFVFNVEYMNCTWQSSSEPQPTNLTLHYWYKNSDNDKVQKCSHYLFSEEITSGCQLQKKEIHLYQTFVVQLQDPREPRRQATQMLKLQNLVIPWAPENLTLHKLSESQLELNWNNRFLNHCLEHLVQYRTDWDHSWTEQSVDYRHKFSLPSVDGQKRYTFRVRSRFNPLCGSAQHWSEWSHPIHWGSNTSKEN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 4 polymer

描述 description	Interleukin-2 receptor alpha chain
分子量 formula_weight	24573.5 kDa
突变 mutation	N68Q
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

ELCDDDPPEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQCTSSATRQTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYHFVVGQMVYYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQASPEGRPESETSCLVTTTDFQIQTEMAATMETSIFTTE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 5 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 7 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	171

▼

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d2b5ia_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.26 — 4-helical cytokines
超家族 Superfamily superfamily	a.26.1 — 4-helical cytokines
家族 Family family	a.26.1.2 — Short-chain cytokines

结构域编号 domain_id	d2b5ib1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.2 — Fibronectin type III
家族 Family family	b.1.2.1 — Fibronectin type III

结构域编号 domain_id	d2b5ib2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.2 — Fibronectin type III
家族 Family family	b.1.2.1 — Fibronectin type III

结构域编号 domain_id	d2b5ic1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.2 — Fibronectin type III
家族 Family family	b.1.2.1 — Fibronectin type III

结构域编号 domain_id	d2b5ic2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.2 — Fibronectin type III
家族 Family family	b.1.2.1 — Fibronectin type III

结构域编号 domain_id	d2b5id1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.18 — Complement control module/SCR domain
超家族 Superfamily superfamily	g.18.1 — Complement control module/SCR domain
家族 Family family	g.18.1.1 — Complement control module/SCR domain

结构域编号 domain_id	d2b5id2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.18 — Complement control module/SCR domain
超家族 Superfamily superfamily	g.18.1 — Complement control module/SCR domain
家族 Family family	g.18.1.1 — Complement control module/SCR domain

CATH v4.4 (7 domains)

结构域编号 domain_id	2b5iA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2b5iB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2b5iB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2b5iC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2b5iC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2b5iD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	70 — Complement Module; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Complement Module, domain 1

结构域编号 domain_id	2b5iD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	230 —

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	113.913 Å
晶胞边长 b length_b	87.709 Å
晶胞边长 c length_c	130.177 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	116.32 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2253
R_work r_work	0.2230
R_free r_free	0.2688

fit	/app/data/saxs_computation/b5/2b5i/2b5i.fit
pddf	/app/data/pr_computation/b5/2b5i/2b5i.pr.out
profile	/app/data/saxs_computation/b5/2b5i/2b5i.dat

cytokine receptor complex

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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. 实体与聚合体信息 (7)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 branched

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)