2abj

;Crystal structure of human branched chain amino acid transaminase in a complex with an inhibitor, C16H10N2O4F3SCl, and pyridoxal 5' phosphate. ;

Method: X-RAY DIFFRACTION D_max: 132.3 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	2abj
沉积日期 deposition_date	2005-07-15
结构标题 title	;Crystal structure of human branched chain amino acid transaminase in a complex with an inhibitor, C16H10N2O4F3SCl, and pyridoxal 5' phosphate. ;
关键词 keywords	;branched-chain-amino-acid aminotransferase, cytosolic, pyridoxal-phosphate-dependent aminotransferase, PLP-Lys220 Schiff base, inhibitor-bound, TRANSFERASE ;; TRANSFERASE
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	39.83 Å
回转半径 Rg (电子) rg_electron	39.42 Å
零角强度 I(0) i0	390417000.00
分子量 molecular_weight	165170.0 kDa
排除体积 excluded_volume	207940 Å³
包络体积 envelope_volume	262150 Å³
水化壳体积 shell_volume	55393 Å³
包络直径 envelope_diameter	138.1 Å
壳层 Rg shell_rg	45.15 Å
包络 Rg envelope_rg	38.98 Å
形状 Rg shape_rg	39.43 Å
总 Rg total_rg	39.71 Å
总原子数 total_atoms	11624
残基数 n_residues	1449
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	132.3 Å
Rg (实空间) rg_real	39.88 Å
Rg 误差 (实空间) rg_real_error	1.10 Å
I(0) (实空间) i0_real	3.9040e+08
I(0) 误差 (实空间) i0_real_error	6.6120e+06
Rg (倒空间) rg_reciprocal	39.86 Å
I(0) (倒空间) i0_reciprocal	390400000.0000
解质量估计 total_estimate	0.8902
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	43.0 Å
偏度 Skewness skewness	0.305
峰度 Kurtosis kurtosis	-0.569
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	89560000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.904

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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	Branched-chain-amino-acid aminotransferase, cytosolic
分子量 formula_weight	41103.9 kDa
EC 编号 ec_number	2.6.1.42
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,G,J
原子数 atom_count	13037

VVGTFKAKDLIVTPATILKEKPDPNNLVFGTVFTDHMLTVEWSSEFGWEKPHIKPLQNLSLHPGSSALHYAVELFEGLKAFRGVDNKIRLFQPNLNMDRMYRSAVRATLPVFDKEELLECIQQLVKLDQEWVPYSTSASLYIRPAFIGTEPSLGVKKPTKALLFVLLSPVGPYFSSGTFNPVSLWANPKYVRAWKGGTGDCKMGGNYGSSLFAQCEDVDNGCQQVLWLYGRDHQITEVGTMNLFLYWINEDGEEELATPPLDGIILPGVTRRCILDLAHQWGEFKVSERYLTMDDLTTALEGNRVREMFSSGTACVVCPVSDILYKGETIHIPTMENGPKLASRILSKLTDIQYGREESDWTIVLS

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
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	N'-(5-CHLOROBENZOFURAN-2-CARBONYL)-2-(TRIFLUOROMETHYL)BENZENESULFONOHYDRAZIDE
分子量 formula_weight	418.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	PYRIDOXAL-5'-PHOSPHATE
分子量 formula_weight	247.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	1413

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2abja_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

结构域编号 domain_id	d2abjd_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

结构域编号 domain_id	d2abjg_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

结构域编号 domain_id	d2abjj_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
超家族 Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
家族 Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

CATH v4.4 (8 domains)

结构域编号 domain_id	2abjA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

结构域编号 domain_id	2abjA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

结构域编号 domain_id	2abjD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

结构域编号 domain_id	2abjD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

结构域编号 domain_id	2abjG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

结构域编号 domain_id	2abjG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

结构域编号 domain_id	2abjJ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

结构域编号 domain_id	2abjJ02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	110.327 Å
晶胞边长 b length_b	114.517 Å
晶胞边长 c length_c	148.869 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	16

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	2.200 Å
最低分辨率 resolution_low	90.910 Å
R 因子 r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2570

fit	/app/data/saxs_computation/ab/2abj/2abj.fit
pddf	/app/data/pr_computation/ab/2abj/2abj.pr.out
profile	/app/data/saxs_computation/ab/2abj/2abj.dat