1qb1

;Bovine Trypsin with 1-[2-[5-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5-dihydro-1-methyl-1H-imidazol-2-yl)phenoxy]pyridin-4-yl]piperidine-3-carboxylic Acid (ZK-806974) ;

Method: X-RAY DIFFRACTION D_max: 53.5 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	1qb1
沉积日期 deposition_date	1999-04-28
结构标题 title	;Bovine Trypsin with 1-[2-[5-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5-dihydro-1-methyl-1H-imidazol-2-yl)phenoxy]pyridin-4-yl]piperidine-3-carboxylic Acid (ZK-806974) ;
关键词 keywords	HYDROLASE, SERINE PROTEINASE, PROTEIN-INHIBITOR COMPLEX, S1 POCKET, FACTOR XA; HYDROLASE
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	17.21 Å
回转半径 Rg (电子) rg_electron	16.09 Å
零角强度 I(0) i0	10995400.00
分子量 molecular_weight	23917.0 kDa
排除体积 excluded_volume	29579 Å³
包络体积 envelope_volume	32731 Å³
水化壳体积 shell_volume	16723 Å³
包络直径 envelope_diameter	53.6 Å
壳层 Rg shell_rg	22.49 Å
包络 Rg envelope_rg	16.34 Å
形状 Rg shape_rg	16.07 Å
总 Rg total_rg	17.12 Å
总原子数 total_atoms	1671
残基数 n_residues	223
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	53.5 Å
Rg (实空间) rg_real	17.09 Å
Rg 误差 (实空间) rg_real_error	0.24 Å
I(0) (实空间) i0_real	1.1000e+07
I(0) 误差 (实空间) i0_real_error	1.2300e+05
Rg (倒空间) rg_reciprocal	17.10 Å
I(0) (倒空间) i0_reciprocal	11000000.0000
解质量估计 total_estimate	0.8949
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	22.5 Å
偏度 Skewness skewness	0.114
峰度 Kurtosis kurtosis	-0.461
角度范围 angular_range	— – 0.4600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3280000.0000
实空间数据点数 n_real_points	77
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.960

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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	PROTEIN (TRYPSIN)
分子量 formula_weight	23324.3 kDa
EC 编号 ec_number	3.4.21.4
来源方法 src_method	nat
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	1895

IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	;1-[2-[5-[AMINO(IMINO)METHYL]-2-HYDROXYPHENOXY]-6-[3-(4,5-DIHYDRO-1-METHYL-1H-IMIDAZOL-2-YL)PHENOXY] PYRIDIN-4-YL]PIPERIDINE-3-CARBOXYLIC ACID ;
分子量 formula_weight	565.5 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	218

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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	d1qb1a_
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	1qb1A01
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	1qb1A02
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 (9)

Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin.

Acta Crystallogr.,Sect.D (1999)

PMID: 10417407 · DOI: 10.1107/S0907444999007350 PRIMARY

Design, Synthesis, and Activity of 2,6-Diphenoxypyridine-Derived Factor Xa Inhibitors

J.Med.Chem. (1999)

DOI: 10.1021/jm980667k

;Discovery of N-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-3,5- Difluoro-6-[3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy] Pyridin-4-Yl-N-Methylglycine (Zk-807834): A Potent, Selective and Orally Active Inhibitor of the Blood Coagulation Enzyme Factor Xa ;

J.Med.Chem. (1998)

DOI: 10.1021/jm980280h

X-Ray Structure of Active Site-Inhibited Clotting Factor Xa. Implications for Drug Design and Substrate Recognition

J.Biol.Chem. (1996)

DOI: 10.1074/jbc.271.47.29988

;Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin ;

FEBS Lett. (1995)

DOI: 10.1016/0014-5793(95)01190-P

Structure of Human Des(1-45) Factor Xa at 2.2 A Resolution

J.Mol.Biol. (1993)

DOI: 10.1006/jmbi.1993.1441

;Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N Alpha-(3-Methyl-1,2,3,4-Tetrahydro-8-Quinolinesulphonyl)- L-Arginyl]-2-Piperidine to Carboxylic Acid (Mqpa) Human Alpha-Thrombin. X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap-Thrombin and Mqpa-Thrombin ;

Eur.J.Biochem. (1990)

;Crystal Structure of Bovine Beta-Trypsin at 1.5 A Resolution in a Crystal Form with Low Molecular Packing Density. Active Site Geometry, Ion Pairs and Solvent Structure ;

J.Mol.Biol. (1989)

Crystal Structure Analysis and Refinement of Two Variants of Trigonal Trypsinogen

FEBS Lett. (1978)

DOI: 10.1016/0014-5793(78)80382-2

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晶胞边长 a length_a	63.160 Å
晶胞边长 b length_b	63.780 Å
晶胞边长 c length_c	69.350 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	1.800 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	0.1830
R_free r_free	0.2370

fit	/app/data/saxs_computation/qb/1qb1/1qb1.fit
pddf	/app/data/pr_computation/qb/1qb1/1qb1.pr.out
profile	/app/data/saxs_computation/qb/1qb1/1qb1.dat