2ajd

Porcine dipeptidyl peptidase IV (CD26) in complex with L-Pro-boro-L-Pro (boroPro)

Method: X-RAY DIFFRACTION D_max: 169.8 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	2ajd
沉积日期 deposition_date	2005-08-01
结构标题 title	Porcine dipeptidyl peptidase IV (CD26) in complex with L-Pro-boro-L-Pro (boroPro)
关键词 keywords	;Serine protease, dipeptidyl peptidase, alpha/beta-hydrolase, beta-propeller, oxyanion hole, substrate channeling, drug design, diabetes mellitus, flexibility, HYDROLASE ;; 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	53.94 Å
回转半径 Rg (电子) rg_electron	53.50 Å
零角强度 I(0) i0	1668600000.00
分子量 molecular_weight	345600.0 kDa
排除体积 excluded_volume	432030 Å³
包络体积 envelope_volume	606700 Å³
水化壳体积 shell_volume	90183 Å³
包络直径 envelope_diameter	166.7 Å
壳层 Rg shell_rg	62.23 Å
包络 Rg envelope_rg	51.54 Å
形状 Rg shape_rg	53.43 Å
总 Rg total_rg	53.97 Å
总原子数 total_atoms	24428
残基数 n_residues	2912
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	169.8 Å
Rg (实空间) rg_real	53.78 Å
Rg 误差 (实空间) rg_real_error	1.62 Å
I(0) (实空间) i0_real	1.6690e+09
I(0) 误差 (实空间) i0_real_error	3.3550e+07
Rg (倒空间) rg_reciprocal	54.04 Å
I(0) (倒空间) i0_reciprocal	1669000000.0000
解质量估计 total_estimate	0.8765
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	82.0 Å
偏度 Skewness skewness	0.080
峰度 Kurtosis kurtosis	-0.766
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	419700000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.624

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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 (7)

Entity 1 polymer

描述 description	Dipeptidyl peptidase 4
分子量 formula_weight	84429.3 kDa
EC 编号 ec_number	3.4.14.5
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	25139

SRRTYTLTDYLKSTFRVKFYTLQWISDHEYLYKQENNILLFNAEYGNSSIFLENSTFDELGYSTNDYSVSPDRQFILFEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWITWSPVGHKLAYVWNNDIYVKNEPNLSSQRITWTGKENVIYNGVTDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRIPYPKAGAENPTVKFFVVDTRTLSPNASVTSYQIVPPASVLIGDHYLCGVTWVTEERISLQWIRRAQNYSIIDICDYDESTGRWISSVARQHIEISTTGWVGRFRPAEPHFTSDGNSFYKIISNEEGYKHICHFQTDKSNCTFITKGAWEVIGIEALTSDYLYYISNEHKGMPGGRNLYRIQLNDYTKVTCLSCELNPERCQYYSASFSNKAKYYQLRCFGPGLPLYTLHSSSSDKELRVLEDNSALDKMLQDVQMPSKKLDVINLHGTKFWYQMILPPHFDKSKKYPLLIEVYAGPCSQKVDTVFRLSWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEATRQFSKMGFVDDKRIAIWGWSYGGYVTSMVLGAGSGVFKCGIAVAPVSKWEYYDSVYTERYMGLPTPEDNLDYYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQLSKALVDAGVDFQTMWYTDEDHGIASNMAHQHIYTHMSHFLKQCFSLP

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	7

Entity 3 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	15

Entity 5 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	(2R)-N-[(2R)-2-(DIHYDROXYBORYL)-1-L-PROLYLPYRROLIDIN-2-YL]-N-[(5R)-5-(DIHYDROXYBORYL)-1-L-PROLYLPYRROLIDIN-2-YL]-L-PROLINAMIDE
分子量 formula_weight	212.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 7 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	711

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2ajda1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.70 — 8-bladed beta-propeller
超家族 Superfamily superfamily	b.70.3 — DPP6 N-terminal domain-like
家族 Family family	b.70.3.1 — DPP6 N-terminal domain-like

结构域编号 domain_id	d2ajda2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.24 — DPP6 catalytic domain-like

结构域编号 domain_id	d2ajdb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.70 — 8-bladed beta-propeller
超家族 Superfamily superfamily	b.70.3 — DPP6 N-terminal domain-like
家族 Family family	b.70.3.1 — DPP6 N-terminal domain-like

结构域编号 domain_id	d2ajdb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.24 — DPP6 catalytic domain-like

结构域编号 domain_id	d2ajdc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.70 — 8-bladed beta-propeller
超家族 Superfamily superfamily	b.70.3 — DPP6 N-terminal domain-like
家族 Family family	b.70.3.1 — DPP6 N-terminal domain-like

结构域编号 domain_id	d2ajdc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.24 — DPP6 catalytic domain-like

结构域编号 domain_id	d2ajdd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.70 — 8-bladed beta-propeller
超家族 Superfamily superfamily	b.70.3 — DPP6 N-terminal domain-like
家族 Family family	b.70.3.1 — DPP6 N-terminal domain-like

结构域编号 domain_id	d2ajdd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.24 — DPP6 catalytic domain-like

CATH v4.4 (8 domains)

结构域编号 domain_id	2ajdA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	140 — 8 Propeller
拓扑 Topology topology	10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily	30 — Dipeptidylpeptidase IV, N-terminal domain

结构域编号 domain_id	2ajdA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	2ajdB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	140 — 8 Propeller
拓扑 Topology topology	10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily	30 — Dipeptidylpeptidase IV, N-terminal domain

结构域编号 domain_id	2ajdB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	2ajdC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	140 — 8 Propeller
拓扑 Topology topology	10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily	30 — Dipeptidylpeptidase IV, N-terminal domain

结构域编号 domain_id	2ajdC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

结构域编号 domain_id	2ajdD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	140 — 8 Propeller
拓扑 Topology topology	10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily	30 — Dipeptidylpeptidase IV, N-terminal domain

结构域编号 domain_id	2ajdD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	63.400 Å
晶胞边长 b length_b	122.070 Å
晶胞边长 c length_c	134.030 Å
晶胞夹角 α angle_alpha	111.41 °
晶胞夹角 β angle_beta	95.27 °
晶胞夹角 γ angle_gamma	94.52 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.560 Å
最低分辨率 resolution_low	19.990 Å
R 因子 r_factor	—
R_work r_work	0.2460
R_free r_free	0.3120

fit	/app/data/saxs_computation/aj/2ajd/2ajd.fit
pddf	/app/data/pr_computation/aj/2ajd/2ajd.pr.out
profile	/app/data/saxs_computation/aj/2ajd/2ajd.dat