SAXSdb — 1hhh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hhh
沉积日期 deposition_date	1993-06-30
结构标题 title	THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2
关键词 keywords	HISTOCOMPATIBILITY ANTIGEN; HISTOCOMPATIBILITY ANTIGEN
实验方法 method	X-RAY DIFFRACTION

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

回转半径 Rg (Guinier) rg_guinier	24.15 Å
回转半径 Rg (电子) rg_electron	22.93 Å
零角强度 I(0) i0	36213900.00
分子量 molecular_weight	44816.0 kDa
排除体积 excluded_volume	55308 Å³
包络体积 envelope_volume	67370 Å³
水化壳体积 shell_volume	24585 Å³
包络直径 envelope_diameter	77.1 Å
壳层 Rg shell_rg	29.76 Å
包络 Rg envelope_rg	23.00 Å
形状 Rg shape_rg	22.91 Å
总 Rg total_rg	23.80 Å
总原子数 total_atoms	3167
残基数 n_residues	385
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

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

最大尺寸 Dmax dmax	82.2 Å
Rg (实空间) rg_real	24.08 Å
Rg 误差 (实空间) rg_real_error	0.70 Å
I(0) (实空间) i0_real	3.6210e+07
I(0) 误差 (实空间) i0_real_error	5.1570e+05
Rg (倒空间) rg_reciprocal	24.10 Å
I(0) (倒空间) i0_reciprocal	36210000.0000
解质量估计 total_estimate	0.8068
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	29.6 Å
偏度 Skewness skewness	0.234
峰度 Kurtosis kurtosis	-0.488
角度范围 angular_range	— – 0.3300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9709000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.000

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

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5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A*0201) (ALPHA CHAIN)
分子量 formula_weight	31854.2 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	3167

GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

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	Escherichia coli

Entity 2 polymer

描述 description	BETA 2-MICROGLOBULIN
分子量 formula_weight	11879.4 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	B

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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	Escherichia coli

Entity 3 polymer

描述 description	HEPATITIS B NUCLEOCAPSID PROTEIN (RESIDUES 18-27)
分子量 formula_weight	1155.3 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	C

FLPSDFFPSV

来源 Source

来源生物 organism	Hepatitis B virus
NCBI 分类编号 ncbi_taxonomy_id	10407

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1hhha1
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	d1hhha2
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	d1hhhb2
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	d1hhhb3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

结构域编号 domain_id	1hhhA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

结构域编号 domain_id	1hhhA02
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	1hhhB00
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

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7. 引用文献 (8)

The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2.

Cell(Cambridge,Mass.) (1993)

PMID: 7694806 · DOI: 10.1016/0092-8674(93)90490-H PRIMARY

Definition of a Minimal Optimal Cytotoxic T-Cell Epitope within the Hepatitis B Virus Nucleocapsid Protein

J.Virol. (1993)

;Hla-A2-Peptide Complexes: Refolding and Crystallization of Molecules Expressed in Escherichia Coli and Complexed with Single Antigenic Peptides ;

Proc.Natl.Acad.Sci.USA (1992)

;The Three-Dimensional Structure of Hla-B27 at 2.1 Angstroms Resolution Suggests a General Mechanism for Tight Peptide Binding to Mhc ;

Cell(Cambridge,Mass.) (1992)

Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution

J.Mol.Biol. (1991)

Structure of the Human Class I Histocompatibility Antigen, Hla-A2

Nature (1987)

The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens

Nature (1987)

Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes

J.Mol.Biol. (1985)

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晶胞边长 a length_a	60.630 Å
晶胞边长 b length_b	81.240 Å
晶胞边长 c length_c	94.760 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.2860
R_work r_work	0.2860
R_free r_free	—

fit	/app/data/saxs_computation/hh/1hhh/1hhh.fit
pddf	/app/data/pr_computation/hh/1hhh/1hhh.pr.out
profile	/app/data/saxs_computation/hh/1hhh/1hhh.dat

THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2

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

5. 实体与聚合体信息 (3)

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

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. 引用文献 (8)

8. 文件与曲线 (10)

Files (7)

Curves (3)