1ppb

;THE REFINED 1.9 ANGSTROMS CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN: INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE AND SIGNIFICANCE OF THE TYR-PRO-PRO-TRP INSERTION SEGMENT ;

Method: X-RAY DIFFRACTION D_max: 57.6 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	1ppb
沉积日期 deposition_date	1991-10-24
结构标题 title	;THE REFINED 1.9 ANGSTROMS CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN: INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE AND SIGNIFICANCE OF THE TYR-PRO-PRO-TRP INSERTION SEGMENT ;
关键词 keywords	SERINE PROTEINASE, HYDROLASE-hydrolase inhibitor complex; HYDROLASE/hydrolase inhibitor
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	19.06 Å
回转半径 Rg (电子) rg_electron	18.05 Å
零角强度 I(0) i0	38211500.00
分子量 molecular_weight	31844.0 kDa
排除体积 excluded_volume	30702 Å³
包络体积 envelope_volume	48350 Å³
水化壳体积 shell_volume	21436 Å³
包络直径 envelope_diameter	59.2 Å
壳层 Rg shell_rg	25.29 Å
包络 Rg envelope_rg	18.44 Å
形状 Rg shape_rg	18.04 Å
总 Rg total_rg	18.78 Å
总原子数 total_atoms	2410
残基数 n_residues	246
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	57.6 Å
Rg (实空间) rg_real	18.90 Å
Rg 误差 (实空间) rg_real_error	0.18 Å
I(0) (实空间) i0_real	3.8210e+07
I(0) 误差 (实空间) i0_real_error	4.1510e+05
Rg (倒空间) rg_reciprocal	18.92 Å
I(0) (倒空间) i0_reciprocal	38210000.0000
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	24.8 Å
偏度 Skewness skewness	0.097
峰度 Kurtosis kurtosis	-0.451
角度范围 angular_range	— – 0.4150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12010000.0000
实空间数据点数 n_real_points	73
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.952

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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	ALPHA-THROMBIN (SMALL SUBUNIT)
分子量 formula_weight	4096.5 kDa
EC 编号 ec_number	3.4.21.5
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	L
原子数 atom_count	2819

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

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

Entity 2 polymer

描述 description	ALPHA-THROMBIN (LARGE SUBUNIT)
分子量 formula_weight	29780.2 kDa
EC 编号 ec_number	3.4.21.5
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	H

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

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

Entity 3 non-polymer

描述 description	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
分子量 formula_weight	454.0 kDa
来源方法 src_method	syn
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	409

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6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1ppb.1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.47 — Trypsin-like serine proteases
超家族 Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
家族 Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (2 domains)

结构域编号 domain_id	1ppbH01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	1ppbH02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

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7. 引用文献 (13)

;The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment. ;

EMBO J. (1989)

PMID: 2583108 PRIMARY

The Spatial Structure of Thrombin as a Guide to its Multiple Sites of Interaction

Semin.Thromb.Hemostasis (1993)

The Electrostatic Properties of Thrombin: Importance for Structural Stabilization and Ligand Binding

Semin.Thromb.Hemostasis (1993)

;The Refined 1.9-Angstroms Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin. Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Properties ;

Protein Sci. (1992)

Electrostatic Interactions in the Association of Proteins: An Analysis of the Thrombin-Hirudin Complex

Protein Sci. (1992)

;Refined 2.3 Angstroms X-Ray Crystal Structure of Bovine Thrombin Complexes Formed with the Benzamidine and Arginine-Based Thrombin Inhibitors Napap, 4-Tapap and Mqpa. A Starting Point for Improving Anti-Thrombotics ;

J.Mol.Biol. (1992)

The Interaction of Thrombin with Fibrinogen. A Structural Basis for its Specificity

Eur.J.Biochem. (1992)

X-Ray Crystal Structures of Human Alpha-Thrombin and of the Human Thrombin-Hirudin Complex

Thrombin: Structure and Function (1992)

Refined Structure of the Hirudin-Thrombin Complex

J.Mol.Biol. (1991)

The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin

Science (1990)

Crystal Structure of the Thrombin-Hirudin Complex: A Novel Mode of Serine Protease Inhibition

Embo J. (1990)

Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophe

Eur.J.Biochem. (1990)

Human D-Phe-Pro-Arg-Ch2-Alpha-Thrombin Crystallization and Diffraction Data

J.Mol.Biol. (1989)

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晶胞边长 a length_a	87.740 Å
晶胞边长 b length_b	67.810 Å
晶胞边长 c length_c	61.070 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	1.920 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.1560
R_work r_work	0.1560
R_free r_free	—

fit	/app/data/saxs_computation/pp/1ppb/1ppb.fit
pddf	/app/data/pr_computation/pp/1ppb/1ppb.pr.out
profile	/app/data/saxs_computation/pp/1ppb/1ppb.dat

;THE REFINED 1.9 ANGSTROMS CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN: INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE AND SIGNIFICANCE OF THE TYR-PRO-PRO-TRP INSERTION SEGMENT ;

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 (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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. 引用文献 (13)

8. 文件与曲线 (10)

Files (7)

Curves (3)