8sk5

Crystal structure of the SARS-CoV-2 neutralizing VHH 7A9 bound to the spike receptor binding domain

Method: X-RAY DIFFRACTION D_max: 72.5 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8sk5
沉积日期 deposition_date	2023-04-18
结构标题 title	Crystal structure of the SARS-CoV-2 neutralizing VHH 7A9 bound to the spike receptor binding domain
关键词 keywords	VHH, Complex, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
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	22.13 Å
回转半径 Rg (电子) rg_electron	21.08 Å
零角强度 I(0) i0	23639500.00
分子量 molecular_weight	36255.0 kDa
排除体积 excluded_volume	44958 Å³
包络体积 envelope_volume	53910 Å³
水化壳体积 shell_volume	21516 Å³
包络直径 envelope_diameter	74.4 Å
壳层 Rg shell_rg	27.50 Å
包络 Rg envelope_rg	21.33 Å
形状 Rg shape_rg	21.03 Å
总 Rg total_rg	22.05 Å
总原子数 total_atoms	2557
残基数 n_residues	327
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	72.5 Å
Rg (实空间) rg_real	22.04 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	2.3640e+07
I(0) 误差 (实空间) i0_real_error	3.0690e+05
Rg (倒空间) rg_reciprocal	22.06 Å
I(0) (倒空间) i0_reciprocal	23640000.0000
解质量估计 total_estimate	0.8971
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	27.0 Å
偏度 Skewness skewness	0.209
峰度 Kurtosis kurtosis	-0.489
角度范围 angular_range	— – 0.3600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5326000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.977

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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 (4)

Entity 1 polymer

描述 description	Spike protein S1
分子量 formula_weight	26095.3 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	A
原子数 atom_count	2732

RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFSGHHHHHH

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
NCBI 分类编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	anti-SARS-CoV-2 receptor binding domain VHH
分子量 formula_weight	18224.8 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

QVQLVESGGGLVQAGGSLRLSCSASGGTASRSAMGWFRQAPGKEREFVAGISRRNSGSTYVADSYEDSVKGRFTISRDNAKNTIYLQMNSLKPEDTAVYYCAAEPTLGWYVPRRSVEYEYWGQGTQVTVSSAAADYKDHDGDYKDHDIDYKDDDDKGAAHHHHHH

来源 Source

来源生物 organism	Lama glama
通用名 common_name	llama
NCBI 分类编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Homo sapiens

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	570.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	157

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6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	8sk5B01
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 (1)

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晶胞边长 a length_a	93.903 Å
晶胞边长 b length_b	93.903 Å
晶胞边长 c length_c	121.386 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	trigonal

分辨率 resolution	2.011 Å
最低分辨率 resolution_low	36.230 Å
R 因子 r_factor	0.1845
R_work r_work	0.1832
R_free r_free	0.2109

fit	/app/data/saxs_computation/sk/8sk5/8sk5.fit
pddf	/app/data/pr_computation/sk/8sk5/8sk5.pr.out
profile	/app/data/saxs_computation/sk/8sk5/8sk5.dat

Crystal structure of the SARS-CoV-2 neutralizing VHH 7A9 bound to the spike receptor binding domain

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 branched

Entity 4 water

6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)