1lnu

CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IAb BOUND TO EALPHA3K PEPTIDE

Method: X-RAY DIFFRACTION D_max: 162.9 Å Quality: GOOD

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	1lnu
沉积日期 deposition_date	2002-05-03
结构标题 title	CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IAb BOUND TO EALPHA3K PEPTIDE
关键词 keywords	Protein-peptide complex, T cell receptor, antigen presentation, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	49.76 Å
回转半径 Rg (电子) rg_electron	49.55 Å
零角强度 I(0) i0	509276000.00
分子量 molecular_weight	184330.0 kDa
排除体积 excluded_volume	229330 Å³
包络体积 envelope_volume	349600 Å³
水化壳体积 shell_volume	61056 Å³
包络直径 envelope_diameter	157.8 Å
壳层 Rg shell_rg	51.13 Å
包络 Rg envelope_rg	48.24 Å
形状 Rg shape_rg	49.51 Å
总 Rg total_rg	49.72 Å
总原子数 total_atoms	13028
残基数 n_residues	1596
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	162.9 Å
Rg (实空间) rg_real	49.83 Å
Rg 误差 (实空间) rg_real_error	1.66 Å
I(0) (实空间) i0_real	5.0930e+08
I(0) 误差 (实空间) i0_real_error	1.0530e+07
Rg (倒空间) rg_reciprocal	49.76 Å
I(0) (倒空间) i0_reciprocal	509200000.0000
解质量估计 total_estimate	0.8294
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	61.1 Å
偏度 Skewness skewness	0.213
峰度 Kurtosis kurtosis	-0.690
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30860000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.000

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	H-2 class II histocompatibility antigen, A-B alpha chain
分子量 formula_weight	20598.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G
原子数 atom_count	13265

IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	H-2 class II histocompatibility antigen, A beta chain
分子量 formula_weight	24938.8 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H

FEAQKAKANKAVDGGGGSLVPRGSGGGGSERHFVYQFMGECYFTNGTQRIRYVTRYIYNREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWKA

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 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	12

Entity 4 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	237

▼

6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d1lnua1
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.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1lnua2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1lnub1
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.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1lnub2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1lnuc1
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.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1lnuc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1lnud1
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.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1lnud2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1lnue1
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.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1lnue2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1lnuf1
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.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1lnuf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1lnug1
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.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1lnug2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1lnuh1
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.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1lnuh2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

CATH v4.4 (16 domains)

结构域编号 domain_id	1lnuA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1lnuA02
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	1lnuB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1lnuB02
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	1lnuC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1lnuC02
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	1lnuD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1lnuD02
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	1lnuE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1lnuE02
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	1lnuF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1lnuF02
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	1lnuG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1lnuG02
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	1lnuH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1lnuH02
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

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	65.040 Å
晶胞边长 b length_b	274.180 Å
晶胞边长 c length_c	65.120 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.42 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	38.390 Å
R 因子 r_factor	—
R_work r_work	0.2110
R_free r_free	0.2450

fit	/app/data/saxs_computation/ln/1lnu/1lnu.fit
pddf	/app/data/pr_computation/ln/1lnu/1lnu.pr.out
profile	/app/data/saxs_computation/ln/1lnu/1lnu.dat

CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IAb BOUND TO EALPHA3K PEPTIDE

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)