1xka

;FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S)-(3'-AMIDINO-3-BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID ;

Method: X-RAY DIFFRACTION D_max: 86.6 Å Quality: REASONABLE

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	1xka
沉积日期 deposition_date	1998-03-19
结构标题 title	;FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S)-(3'-AMIDINO-3-BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID ;
关键词 keywords	BLOOD COAGULATION FACTOR, SERINE PROTEINASE, EPIDERMAL GROWTH FACTOR LIKE DOMAIN; BLOOD COAGULATION FACTOR
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	23.43 Å
回转半径 Rg (电子) rg_electron	22.79 Å
零角强度 I(0) i0	25287300.00
分子量 molecular_weight	36956.0 kDa
排除体积 excluded_volume	45517 Å³
包络体积 envelope_volume	54991 Å³
水化壳体积 shell_volume	21480 Å³
包络直径 envelope_diameter	90.1 Å
壳层 Rg shell_rg	27.89 Å
包络 Rg envelope_rg	23.92 Å
形状 Rg shape_rg	22.73 Å
总 Rg total_rg	23.57 Å
总原子数 total_atoms	2580
残基数 n_residues	318
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	86.6 Å
Rg (实空间) rg_real	23.71 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	2.5290e+07
I(0) 误差 (实空间) i0_real_error	3.8880e+05
Rg (倒空间) rg_reciprocal	23.64 Å
I(0) (倒空间) i0_reciprocal	25290000.0000
解质量估计 total_estimate	0.5764
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.3 Å
偏度 Skewness skewness	0.710
峰度 Kurtosis kurtosis	0.164
角度范围 angular_range	— – 0.3400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4019000.0000
实空间数据点数 n_real_points	66
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.498; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.700; Smooth: 0.949

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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 (5)

Entity 1 polymer

描述 description	BLOOD COAGULATION FACTOR XA
分子量 formula_weight	10386.5 kDa
EC 编号 ec_number	3.4.21.6
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	L
原子数 atom_count	2790

KDGDQCETSPCQNQGKCKDGLGEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLER

Entity 2 polymer

描述 description	BLOOD COAGULATION FACTOR XA
分子量 formula_weight	26604.3 kDa
EC 编号 ec_number	3.4.21.6
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	C

IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTR

Entity 3 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 4 non-polymer

描述 description	;(2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID ;
分子量 formula_weight	388.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	210

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1xkac_
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

结构域编号 domain_id	d1xkal1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

结构域编号 domain_id	d1xkal2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

CATH v4.4 (4 domains)

结构域编号 domain_id	1xkaC01
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	1xkaC02
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	1xkaL01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

结构域编号 domain_id	1xkaL02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

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7. 引用文献 (3)

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晶胞边长 a length_a	61.500 Å
晶胞边长 b length_b	65.800 Å
晶胞边长 c length_c	81.400 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	2.300 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2870

fit	/app/data/saxs_computation/xk/1xka/1xka.fit
pddf	/app/data/pr_computation/xk/1xka/1xka.pr.out
profile	/app/data/saxs_computation/xk/1xka/1xka.dat

;FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S)-(3'-AMIDINO-3-BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID ;

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)