1i1f

Crystal structure of human class i mhc (hla-a2.1) complexed with beta 2-microglobulin and hiv-rt variant peptide i1y

Method: X-RAY DIFFRACTION Dmax: 130.9 Å Quality: REASONABLE

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

PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN, GOGO-A0201 ALPHA CHAIN)

Homo sapiens

UniProt P01892

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 A; UniProt 25–299 片段:PEPTIDE-BINDING DOMAIN + ALPHA3 PROTEIN (BETA 2-MICROGLOBULIN) × 1 (P61769) PROTEIN (HIV-RT VARIANT PEPTIDE I1F (FLKEPVHGV)) × 1 X-RAY DIFFRACTION X-ray结晶条件:pH 6.5;PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 16% PEG8000 IN 25MM MES BUFFER, PH6.5. THE HANGING DROP WAS A 1:1 MIXTURE OF THE RESERVOIR SOLUTION AND THE PROTEIN SOLUTION WHICH CONTAINED 10MG/ML PROTEIN IN 25MM MES BUFFER, PH6.5. 分辨率 2.80 Å R-free 0.315
2 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 D; UniProt 25–299 片段:PEPTIDE-BINDING DOMAIN + ALPHA3 PROTEIN (BETA 2-MICROGLOBULIN) × 1 (P61769) PROTEIN (HIV-RT VARIANT PEPTIDE I1F (FLKEPVHGV)) × 1 X-RAY DIFFRACTION X-ray结晶条件:pH 6.5;PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 16% PEG8000 IN 25MM MES BUFFER, PH6.5. THE HANGING DROP WAS A 1:1 MIXTURE OF THE RESERVOIR SOLUTION AND THE PROTEIN SOLUTION WHICH CONTAINED 10MG/ML PROTEIN IN 25MM MES BUFFER, PH6.5. 分辨率 2.80 Å R-free 0.315

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 271 个其他 PDB 条目、464 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 1A02_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–275; UniProt 25–299 作者链 D; PDB构建体 1–275; UniProt 25–299

PROTEIN (BETA 2-MICROGLOBULIN)

Homo sapiens

UniProt P61769

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 B; UniProt 12–110 片段:BETA 2-MICROGLOBULIN PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN, GOGO-A0201 ALPHA CHAIN) × 1 (P01892) PROTEIN (HIV-RT VARIANT PEPTIDE I1F (FLKEPVHGV)) × 1 X-RAY DIFFRACTION X-ray结晶条件:pH 6.5;PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 16% PEG8000 IN 25MM MES BUFFER, PH6.5. THE HANGING DROP WAS A 1:1 MIXTURE OF THE RESERVOIR SOLUTION AND THE PROTEIN SOLUTION WHICH CONTAINED 10MG/ML PROTEIN IN 25MM MES BUFFER, PH6.5. 分辨率 2.80 Å R-free 0.315
2 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 E; UniProt 12–110 片段:BETA 2-MICROGLOBULIN PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN, GOGO-A0201 ALPHA CHAIN) × 1 (P01892) PROTEIN (HIV-RT VARIANT PEPTIDE I1F (FLKEPVHGV)) × 1 X-RAY DIFFRACTION X-ray结晶条件:pH 6.5;PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 16% PEG8000 IN 25MM MES BUFFER, PH6.5. THE HANGING DROP WAS A 1:1 MIXTURE OF THE RESERVOIR SOLUTION AND THE PROTEIN SOLUTION WHICH CONTAINED 10MG/ML PROTEIN IN 25MM MES BUFFER, PH6.5. 分辨率 2.80 Å R-free 0.315

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 1313 个其他 PDB 条目、1997 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 B2MG_HUMAN
Isoform
PDB实体 2
链与序列区间 作者链 B; PDB构建体 2–100; UniProt 12–110 作者链 E; PDB构建体 2–100; UniProt 12–110

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。

SAXS 散射曲线 SAXS Profile

SAXS profile for 1i1f

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1i1f
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id1i1f
沉积日期 deposition_date1999-04-16
结构标题 titleCrystal structure of human class i mhc (hla-a2.1) complexed with beta 2-microglobulin and hiv-rt variant peptide i1y
关键词 keywordsHUMAN CLASS I MHC, HIV, IMMUNE SYSTEM; IMMUNE SYSTEM
实验方法 methodX-RAY DIFFRACTION

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier40.28
回转半径 Rg (电子) rg_electron40.17
零角强度 I(0) i0129897000.00
分子量 molecular_weight89323.0 kDa
排除体积 excluded_volume110220 ų
包络体积 envelope_volume154080 ų
水化壳体积 shell_volume33267 ų
包络直径 envelope_diameter132.9
壳层 Rg shell_rg43.60
包络 Rg envelope_rg39.03
形状 Rg shape_rg40.17
总 Rg total_rg40.36
总原子数 total_atoms6311
残基数 n_residues768
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax130.9
Rg (实空间) rg_real40.51
Rg 误差 (实空间) rg_real_error1.24
I(0) (实空间) i0_real1.2990e+08
I(0) 误差 (实空间) i0_real_error2.0330e+06
Rg (倒空间) rg_reciprocal40.28
I(0) (倒空间) i0_reciprocal129900000.0000
解质量估计 total_estimate0.6078
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary30.2
偏度 Skewness skewness0.344
峰度 Kurtosis kurtosis-0.829
角度范围 angular_range— – 0.1950 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha9445000.0000
实空间数据点数 n_real_points40
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 0.107; Positv: 1.000; Valcen: 0.608; Smooth: 0.619

5. 晶体学与实验 5. Crystallography & Experiment

6. 实体与聚合物信息 Entities & Polymers (3)

7. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

结构域编号 domain_idd1i1fa1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
结构域编号 domain_idd1i1fa2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.19 — MHC antigen-recognition domain
超家族 Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
家族 Family familyd.19.1.1 — MHC antigen-recognition domain
结构域编号 domain_idd1i1fb2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
结构域编号 domain_idd1i1fb3
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd1i1fd1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
结构域编号 domain_idd1i1fd2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.19 — MHC antigen-recognition domain
超家族 Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
家族 Family familyd.19.1.1 — MHC antigen-recognition domain
结构域编号 domain_idd1i1fe2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
结构域编号 domain_idd1i1fe3
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags

CATH v4.4 (6 domains)

结构域编号 domain_id1i1fA01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
结构域编号 domain_id1i1fA02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id1i1fB00
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id1i1fD01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
结构域编号 domain_id1i1fD02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id1i1fE00
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins

8. 引用文献 (1)

9. 文件与曲线 (10)