SAXSdb — 1hnv

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hnv
沉积日期 deposition_date	1995-03-30
结构标题 title	STRUCTURE OF HIV-1 RT(SLASH)TIBO R 86183 COMPLEX REVEALS SIMILARITY IN THE BINDING OF DIVERSE NONNUCLEOSIDE INHIBITORS
关键词 keywords	NUCLEOTIDYLTRANSFERASE; NUCLEOTIDYLTRANSFERASE
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	35.50 Å
回转半径 Rg (电子) rg_electron	34.71 Å
零角强度 I(0) i0	172575000.00
分子量 molecular_weight	110560.0 kDa
排除体积 excluded_volume	140540 Å³
包络体积 envelope_volume	193460 Å³
水化壳体积 shell_volume	46320 Å³
包络直径 envelope_diameter	119.9 Å
壳层 Rg shell_rg	41.51 Å
包络 Rg envelope_rg	34.12 Å
形状 Rg shape_rg	34.66 Å
总 Rg total_rg	35.42 Å
总原子数 total_atoms	7833
残基数 n_residues	985
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	115.4 Å
Rg (实空间) rg_real	35.42 Å
Rg 误差 (实空间) rg_real_error	1.00 Å
I(0) (实空间) i0_real	1.7260e+08
I(0) 误差 (实空间) i0_real_error	2.8640e+06
Rg (倒空间) rg_reciprocal	35.47 Å
I(0) (倒空间) i0_reciprocal	172600000.0000
解质量估计 total_estimate	0.9030
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	43.6 Å
偏度 Skewness skewness	0.212
峰度 Kurtosis kurtosis	-0.518
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24090000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.957

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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 (3)

Entity 1 polymer

描述 description	HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
分子量 formula_weight	64274.7 kDa
EC 编号 ec_number	2.7.7.49
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	A
原子数 atom_count	7833

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI 分类编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
分子量 formula_weight	49911.4 kDa
EC 编号 ec_number	2.7.7.49
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	B

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWY

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI 分类编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	5-CHLORO-8-METHYL-7-(3-METHYL-BUT-2-ENYL)-6,7,8,9-TETRAHYDRO-2H-2,7,9A-TRIAZA-BENZO[CD]AZULENE-1-THIONE
分子量 formula_weight	321.9 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) 12 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1hnva1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.1 — Ribonuclease H

结构域编号 domain_id	d1hnva2
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.2 — Reverse transcriptase

结构域编号 domain_id	d1hnvb_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.2 — Reverse transcriptase

CATH v4.4 (9 domains)

结构域编号 domain_id	1hnvA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	10 — HIV Type 1 Reverse Transcriptase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — HIV Type 1 Reverse Transcriptase, subunit A, domain 1

结构域编号 domain_id	1hnvA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

结构域编号 domain_id	1hnvA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

结构域编号 domain_id	1hnvA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

结构域编号 domain_id	1hnvA05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

结构域编号 domain_id	1hnvB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	10 — HIV Type 1 Reverse Transcriptase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — HIV Type 1 Reverse Transcriptase, subunit A, domain 1

结构域编号 domain_id	1hnvB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

结构域编号 domain_id	1hnvB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

结构域编号 domain_id	1hnvB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

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7. 引用文献 (8)

Structure of HIV-1 RT/TIBO R 86183 complex reveals similarity in the binding of diverse nonnucleoside inhibitors.

Nat.Struct.Biol. (1995)

PMID: 7545077 · DOI: 10.1038/nsb0595-407 PRIMARY

Structure of HIV-1 Reverse Transcriptase in a Complex with the Nonnucleoside Inhibitor Alpha-Apa R95845 at 2.8 Angstroms Resolution

Structure (1995)

;Buried Surface Analysis of HIV-1 Reverse Transcriptase P66(Slash)P51 Heterodimer and its Interaction with DsDNA Template(Slash)Primer ;

J.Mol.Recog. (1994)

;Locations of Anti-Aids Drug Binding Sites and Resistance Mutations in the Three-Dimensional Structure of HIV-1 Reverse Transcriptase: Implications for Mechanisms of Drug Inhibition and Resistance ;

J.Mol.Biol. (1994)

;Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 Angstroms Resolution Shows Bent DNA ;

Proc.Natl.Acad.Sci.USA (1993)

Review of HIV-1 Reverse Transcriptase Three-Dimensional Structure: Implications for Drug Design

Perspect.Drug Discovery Des. (1993)

Structure of HIV-1 Reverse Transcriptase(Slash)DNA Complex at 7 Angstroms Resolution Showing Active Site Locations

Nature (1992)

;Crystals of a Ternary Complex of Human Immunodeficiency Virus Type 1 Reverse Transcriptase with a Monoclonal Antibody Fab Fragment and Double-Stranded DNA Diffract X-Rays to 3.5 Angstroms Resolution ;

Proc.Natl.Acad.Sci.USA (1991)

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晶胞边长 a length_a	227.200 Å
晶胞边长 b length_b	70.200 Å
晶胞边长 c length_c	105.700 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.60 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2490
R_work r_work	0.2490
R_free r_free	0.3560

fit	/app/data/saxs_computation/hn/1hnv/1hnv.fit
pddf	/app/data/pr_computation/hn/1hnv/1hnv.pr.out
profile	/app/data/saxs_computation/hn/1hnv/1hnv.dat

STRUCTURE OF HIV-1 RT(SLASH)TIBO R 86183 COMPLEX REVEALS SIMILARITY IN THE BINDING OF DIVERSE NONNUCLEOSIDE INHIBITORS

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

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. 引用文献 (8)

8. 文件与曲线 (10)

Files (7)

Curves (3)