1gxd

proMMP-2/TIMP-2 complex

Method: X-RAY DIFFRACTION D_max: 221.4 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	1gxd
沉积日期 deposition_date	2002-04-02
结构标题 title	proMMP-2/TIMP-2 complex
关键词 keywords	;HYDROLASE, METALLOPROTEASE, ZYMOGEN, COLLAGEN DEGRADATION, EXTRACELLULAR MATRIX, GELATINASE A, MATRIX METALLOPROTEINASE 2, PROTEINASE INHIBITOR ;; 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	58.32 Å
回转半径 Rg (电子) rg_electron	60.97 Å
零角强度 I(0) i0	499597000.00
分子量 molecular_weight	183980.0 kDa
排除体积 excluded_volume	229270 Å³
包络体积 envelope_volume	339210 Å³
水化壳体积 shell_volume	55882 Å³
包络直径 envelope_diameter	249.2 Å
壳层 Rg shell_rg	47.37 Å
包络 Rg envelope_rg	63.24 Å
形状 Rg shape_rg	60.87 Å
总 Rg total_rg	60.84 Å
总原子数 total_atoms	12945
残基数 n_residues	1631
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	221.4 Å
Rg (实空间) rg_real	59.78 Å
Rg 误差 (实空间) rg_real_error	3.00 Å
I(0) (实空间) i0_real	4.9920e+08
I(0) 误差 (实空间) i0_real_error	1.1440e+07
Rg (倒空间) rg_reciprocal	56.94 Å
I(0) (倒空间) i0_reciprocal	497200000.0000
解质量估计 total_estimate	0.6636
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	41.0 Å
偏度 Skewness skewness	0.858
峰度 Kurtosis kurtosis	0.225
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0035
最高正则化参数 α highest_alpha	26710000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.260; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.108; Smooth: 0.737

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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	72 KDA TYPE IV COLLAGENASE
分子量 formula_weight	70995.4 kDa
EC 编号 ec_number	3.4.24.24
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	12945

APSPIIKFPGDVAPKTDKELAVQYLNTFYGCPKESCNLFVLKDTLKKMQKFFGLPQTGDLDQNTIETMRKPRCGNPDVANYNFFPRKPKWDKNQITYRIIGYTPDLDPETVDDAFARAFQVWSDVTPLRFSRIHDGEADIMINFGRWEHGDGYPFDGKDGLLAHAFAPGTGVGGDSHFDDDELWTLGEGQVVRVKYGNADGEYCKFPFLFNGKEYNSCTDTGRSDGFLWCSTTYNFEKDGKYGFCPHEALFTMGGNAEGQPCKFPFRFQGTSYDSCTTEGRTDGYRWCGTTEDYDRDKKYGFCPETAMSTVGGNSEGAPCVFPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFCPDQGYSLFLVAAHAFGHAMGLEHSQDPGALMAPIYTYTKNFRLSQDDIKGIQELYGASPDIDLGTGPTPTLGPVTPEICKQDIVFDGIAQIRGEIFFFKDRFIWRTVTPRDKPMGPLLVATFWPELPEKIDAVYEAPQEEKAVFFAGNEYWIYSASTLERGYPKPLTSLGLPPDVQRVDAAFNWSKNKKTYIFAGDKFWRYNEVKKKMDPGFPKLIADAWNAIPDNLDAVVDLQGGGHSYFFKGAYYLKLENQSLKSVKFGSIKSDWLGC

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	TRICHOPLUSIA NI

Entity 2 polymer

描述 description	METALLOPROTEINASE INHIBITOR 2
分子量 formula_weight	21783.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D

CSCSPVHPQQAFCNADVVIRAKAVSEKEVDSGNDIYGNPIKRIQYEIKQIKMFKGPEKDIEFIYTAPSSAVCGVSLDVGGKKEYLIAGKAEGDGKMHITLCDFIVPWDTLSTTQKKSLNHRYQMGCECKITRCPMIPCYISSPDECLWMDWVTEKNINGHQAKFFACIKRSDGSCAWYRGAAPPKQEFLDIEDP

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	TRICHOPLUSIA NI

Entity 3 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	2

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	4

Entity 5 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	2

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6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

结构域编号 domain_id	d1gxda1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.20 — PGBD-like
超家族 Superfamily superfamily	a.20.1 — PGBD-like
家族 Family family	a.20.1.2 — MMP N-terminal domain

结构域编号 domain_id	d1gxda2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.66 — 4-bladed beta-propeller
超家族 Superfamily superfamily	b.66.1 — Hemopexin-like domain
家族 Family family	b.66.1.1 — Hemopexin-like domain

结构域编号 domain_id	d1gxda3
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.92.1.11 — Matrix metalloproteases, catalytic domain

结构域编号 domain_id	d1gxda4
类 Class class	g — Small proteins
折叠类型 Fold fold	g.14 — Kringle-like
超家族 Superfamily superfamily	g.14.1 — Kringle-like
家族 Family family	g.14.1.2 — Fibronectin type II module

结构域编号 domain_id	d1gxda5
类 Class class	g — Small proteins
折叠类型 Fold fold	g.14 — Kringle-like
超家族 Superfamily superfamily	g.14.1 — Kringle-like
家族 Family family	g.14.1.2 — Fibronectin type II module

结构域编号 domain_id	d1gxda6
类 Class class	g — Small proteins
折叠类型 Fold fold	g.14 — Kringle-like
超家族 Superfamily superfamily	g.14.1 — Kringle-like
家族 Family family	g.14.1.2 — Fibronectin type II module

结构域编号 domain_id	d1gxdb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.20 — PGBD-like
超家族 Superfamily superfamily	a.20.1 — PGBD-like
家族 Family family	a.20.1.2 — MMP N-terminal domain

结构域编号 domain_id	d1gxdb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.66 — 4-bladed beta-propeller
超家族 Superfamily superfamily	b.66.1 — Hemopexin-like domain
家族 Family family	b.66.1.1 — Hemopexin-like domain

结构域编号 domain_id	d1gxdb3
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.92.1.11 — Matrix metalloproteases, catalytic domain

结构域编号 domain_id	d1gxdb4
类 Class class	g — Small proteins
折叠类型 Fold fold	g.14 — Kringle-like
超家族 Superfamily superfamily	g.14.1 — Kringle-like
家族 Family family	g.14.1.2 — Fibronectin type II module

结构域编号 domain_id	d1gxdb5
类 Class class	g — Small proteins
折叠类型 Fold fold	g.14 — Kringle-like
超家族 Superfamily superfamily	g.14.1 — Kringle-like
家族 Family family	g.14.1.2 — Fibronectin type II module

结构域编号 domain_id	d1gxdb6
类 Class class	g — Small proteins
折叠类型 Fold fold	g.14 — Kringle-like
超家族 Superfamily superfamily	g.14.1 — Kringle-like
家族 Family family	g.14.1.2 — Fibronectin type II module

结构域编号 domain_id	d1gxdc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.3 — TIMP-like
家族 Family family	b.40.3.1 — Tissue inhibitor of metalloproteinases, TIMP

结构域编号 domain_id	d1gxdd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.3 — TIMP-like
家族 Family family	b.40.3.1 — Tissue inhibitor of metalloproteinases, TIMP

CATH v4.4 (14 domains)

结构域编号 domain_id	1gxdA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1gxdA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

结构域编号 domain_id	1gxdA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

结构域编号 domain_id	1gxdA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

结构域编号 domain_id	1gxdA05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	110 — 4 Propeller
拓扑 Topology topology	10 — Hemopexin
同源超家族 H-superfamily homologous superfamily	10 — Hemopexin-like domain

结构域编号 domain_id	1gxdB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1gxdB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

结构域编号 domain_id	1gxdB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

结构域编号 domain_id	1gxdB04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
同源超家族 H-superfamily homologous superfamily	10 — Fibronectin, type II, collagen-binding

结构域编号 domain_id	1gxdB05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	110 — 4 Propeller
拓扑 Topology topology	10 — Hemopexin
同源超家族 H-superfamily homologous superfamily	10 — Hemopexin-like domain

结构域编号 domain_id	1gxdC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	370 — Tissue inhibitor of metalloproteinase-1. Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tissue inhibitor of metalloproteinase-1. Chain B, domain 1

结构域编号 domain_id	1gxdC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1gxdD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	370 — Tissue inhibitor of metalloproteinase-1. Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tissue inhibitor of metalloproteinase-1. Chain B, domain 1

结构域编号 domain_id	1gxdD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	120 —

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7. 引用文献 (1)

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晶胞边长 a length_a	75.696 Å
晶胞边长 b length_b	374.575 Å
晶胞边长 c length_c	191.000 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.2780
R_work r_work	0.2750
R_free r_free	0.3330

fit	/app/data/saxs_computation/gx/1gxd/1gxd.fit
pddf	/app/data/pr_computation/gx/1gxd/1gxd.pr.out
profile	/app/data/saxs_computation/gx/1gxd/1gxd.dat

proMMP-2/TIMP-2 complex

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 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)