1tmn

;Binding of n-carboxymethyl dipeptide inhibitors to thermolysin determined by x-ray crystallography. a novel class of transition-state analogues for zinc peptidases ;

Method: X-RAY DIFFRACTION D_max: 67.3 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	1tmn
沉积日期 deposition_date	1987-06-29
结构标题 title	;Binding of n-carboxymethyl dipeptide inhibitors to thermolysin determined by x-ray crystallography. a novel class of transition-state analogues for zinc peptidases ;
关键词 keywords	METALLOPROTEINASE, 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	20.37 Å
回转半径 Rg (电子) rg_electron	19.63 Å
零角强度 I(0) i0	39868700.00
分子量 molecular_weight	32707.0 kDa
排除体积 excluded_volume	31584 Å³
包络体积 envelope_volume	48605 Å³
水化壳体积 shell_volume	20786 Å³
包络直径 envelope_diameter	68.4 Å
壳层 Rg shell_rg	26.10 Å
包络 Rg envelope_rg	19.93 Å
形状 Rg shape_rg	19.63 Å
总 Rg total_rg	20.27 Å
总原子数 total_atoms	2472
残基数 n_residues	316
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	67.3 Å
Rg (实空间) rg_real	20.34 Å
Rg 误差 (实空间) rg_real_error	0.34 Å
I(0) (实空间) i0_real	3.9870e+07
I(0) 误差 (实空间) i0_real_error	4.7040e+05
Rg (倒空间) rg_reciprocal	20.35 Å
I(0) (倒空间) i0_reciprocal	39870000.0000
解质量估计 total_estimate	0.8822
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	24.0 Å
偏度 Skewness skewness	0.366
峰度 Kurtosis kurtosis	-0.252
角度范围 angular_range	— – 0.3900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7497000.0000
实空间数据点数 n_real_points	71
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.999

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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	THERMOLYSIN
分子量 formula_weight	34362.3 kDa
EC 编号 ec_number	3.4.24.27
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	E
原子数 atom_count	2616

ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGDGIFTYDAKYRTTLPGSLWADADNQFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAIRSSVHYSQGYNNAFWNGSEMVYGDGDGQTFIPLSGGIDVVAHELTHAVTDYTAGLIYQNESGAINEAISDIFGTLVEFYANKNPDWEIGEDVYTPGISGDSLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKAAYLISQGGTHYGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTSQEVASVKQAFDAVGVK

来源 Source

来源生物 organism	Bacillus thermoproteolyticus
NCBI 分类编号 ncbi_taxonomy_id	1427

Entity 2 non-polymer

描述 description	N-[(1R)-1-carboxy-3-phenylpropyl]-L-leucyl-L-tryptophan
分子量 formula_weight	479.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	4

Entity 4 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 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	144

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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	d1tmne_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.2 — Thermolysin-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1tmnE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	170 — Elastase; domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1tmnE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	390 — Neutral Protease; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Neutral Protease Domain 2

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7. 引用文献 (23)

;Binding of N-carboxymethyl dipeptide inhibitors to thermolysin determined by X-ray crystallography: a novel class of transition-state analogues for zinc peptidases ;

Biochemistry (1984)

PMID: 6395881 · DOI: 10.1021/bi00319a010 PRIMARY

Structures of Two Thermolysin-Inhibitor Complexes that Differ by a Single Hydrogen Bond

Science (1987)

Crystallographic Structural Analysis of Phosphoramidates as Inhibitors and Transition-State Analogs of Thermolysin

Eur.J.Biochem. (1986)

An Interactive Computer Graphics Study of Thermolysin-Catalyzed Peptide Cleavage and Inhibition by N-Carboxymethyl Dipeptides

Biochemistry (1984)

Structural Analysis of the Inhibition of Thermolysin by an Active-Site-Directed Irreversible Inhibitor

Biochemistry (1983)

Structure of a Mercaptan-Thermolysin Complex Illustrates Mode of Inhibition of Zinc Proteases by Substrate-Analogue Mercaptans

Biochemistry (1982)

Structure of Thermolysin Refined at 1.6 Angstroms Resolution

J.Mol.Biol. (1982)

Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis

Biochemistry (1981)

Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography

J.Biol.Chem. (1979)

;A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A Model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates ;

J.Mol.Biol. (1977)

Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis

Biochemistry (1977)

Comparison of the Structures of Carboxypeptidase a and Thermolysin

J.Biol.Chem. (1977)

Role of Calcium in the Thermal Stability of Thermolysin

Biochemistry (1976)

The Structure and Stability of Thermolysin

Experientia,Suppl. (1976)

Evidence of Homologous Relationship between Thermolysin and Neutral Protease a of Bacillus Subtilis

Proc.Natl.Acad.Sci.USA (1975)

The Conformation of Thermolysin

J.Biol.Chem. (1974)

Binding of Lanthanide Ions to Thermolysin

Biochemistry (1974)

The Structure of Thermolysin. An Electron Density Map at 2.3 Angstroms Resolution

J.Mol.Biol. (1972)

Amino-Acid Sequence of Thermolysin

Nature New Biol. (1972)

Three Dimensional Structure of Thermolysin

Nature New Biol. (1972)

Structure of Thermolysin

Nature New Biol. (1972)

The Gamma Turn. Evidence for a New Folded Conformation in Proteins

Macromolecules (1972)

Rare Earths as Isomorphous Calcium Replacements for Protein Crystallography

Biochem.Biophys.Res.Commun. (1972)

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晶胞边长 a length_a	94.200 Å
晶胞边长 b length_b	94.200 Å
晶胞边长 c length_c	131.400 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	14.900 Å
R 因子 r_factor	—
R_work r_work	0.1710
R_free r_free	—

fit	/app/data/saxs_computation/tm/1tmn/1tmn.fit
pddf	/app/data/pr_computation/tm/1tmn/1tmn.pr.out
profile	/app/data/saxs_computation/tm/1tmn/1tmn.dat

;Binding of n-carboxymethyl dipeptide inhibitors to thermolysin determined by x-ray crystallography. a novel class of transition-state analogues for zinc peptidases ;

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

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 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 (23)

8. 文件与曲线 (10)

Files (7)

Curves (3)