SAXSdb — 8dey

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8dey
沉积日期 deposition_date	2022-06-21
结构标题 title	Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709
关键词 keywords	E3 ligase, molecular glue, complex, LIGASE; LIGASE
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	56.67 Å
回转半径 Rg (电子) rg_electron	57.03 Å
零角强度 I(0) i0	1075630000.00
分子量 molecular_weight	275410.0 kDa
排除体积 excluded_volume	345090 Å³
包络体积 envelope_volume	512010 Å³
水化壳体积 shell_volume	77343 Å³
包络直径 envelope_diameter	217.2 Å
壳层 Rg shell_rg	56.65 Å
包络 Rg envelope_rg	56.52 Å
形状 Rg shape_rg	57.01 Å
总 Rg total_rg	57.06 Å
总原子数 total_atoms	19332
残基数 n_residues	2460
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	199.7 Å
Rg (实空间) rg_real	57.32 Å
Rg 误差 (实空间) rg_real_error	2.66 Å
I(0) (实空间) i0_real	1.0760e+09
I(0) 误差 (实空间) i0_real_error	2.4220e+07
Rg (倒空间) rg_reciprocal	56.13 Å
I(0) (倒空间) i0_reciprocal	1074000000.0000
解质量估计 total_estimate	0.7900
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	49.9 Å
偏度 Skewness skewness	0.617
峰度 Kurtosis kurtosis	-0.147
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	125900000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.664; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.804; Smooth: 0.471

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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	Protein cereblon
分子量 formula_weight	42971.6 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	A,D
原子数 atom_count	19332

RTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

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 polymer

描述 description	DNA damage-binding protein 1
分子量 formula_weight	93347.1 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	B,E

MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

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 3 polymer

描述 description	Zinc finger protein Helios
分子量 formula_weight	6543.6 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,F

SERPFHCNQCGASFTQKGNLLRHIKLHSGEKPFKCPFCSYACRRRDALTGHLRTHSV

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 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	6

Entity 5 non-polymer

描述 description	(3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione
分子量 formula_weight	417.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

结构域编号 domain_id	8deyA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
同源超家族 H-superfamily homologous superfamily	40 — LON domain-like

结构域编号 domain_id	8deyA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Peptide methionine sulfoxide reductase.

结构域编号 domain_id	8deyB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	8deyB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	8deyB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	910 —

结构域编号 domain_id	8deyD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
同源超家族 H-superfamily homologous superfamily	40 — LON domain-like

结构域编号 domain_id	8deyD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Peptide methionine sulfoxide reductase.

结构域编号 domain_id	8deyE01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	8deyE02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	8deyE03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	910 —

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7. 引用文献 (1)

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晶胞边长 a length_a	96.476 Å
晶胞边长 b length_b	96.227 Å
晶胞边长 c length_c	155.598 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	93.46 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	3.700 Å
最低分辨率 resolution_low	84.150 Å
R 因子 r_factor	0.3011
R_work r_work	0.2985
R_free r_free	0.3480

fit	/app/data/saxs_computation/de/8dey/8dey.fit
pddf	/app/data/pr_computation/de/8dey/8dey.pr.out
profile	/app/data/saxs_computation/de/8dey/8dey.dat

Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709

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 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

6. 折叠分类 (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)