SAXSdb — 1fkp

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fkp
沉积日期 deposition_date	2000-08-10
结构标题 title	CRYSTAL STRUCTURE OF NNRTI RESISTANT K103N MUTANT HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE
关键词 keywords	HIV-1 reverse transcriptase, AIDS, non-nucleoside inhibitor, nevirapine, drug resistance mutation, drug design, 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	35.44 Å
回转半径 Rg (电子) rg_electron	34.69 Å
零角强度 I(0) i0	170837000.00
分子量 molecular_weight	110420.0 kDa
排除体积 excluded_volume	140540 Å³
包络体积 envelope_volume	189430 Å³
水化壳体积 shell_volume	45385 Å³
包络直径 envelope_diameter	119.1 Å
壳层 Rg shell_rg	41.46 Å
包络 Rg envelope_rg	34.18 Å
形状 Rg shape_rg	34.64 Å
总 Rg total_rg	35.39 Å
总原子数 total_atoms	7814
残基数 n_residues	949
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	115.2 Å
Rg (实空间) rg_real	35.38 Å
Rg 误差 (实空间) rg_real_error	0.87 Å
I(0) (实空间) i0_real	1.7080e+08
I(0) 误差 (实空间) i0_real_error	2.6780e+06
Rg (倒空间) rg_reciprocal	35.42 Å
I(0) (倒空间) i0_reciprocal	170800000.0000
解质量估计 total_estimate	0.9000
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	43.5 Å
偏度 Skewness skewness	0.228
峰度 Kurtosis kurtosis	-0.488
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	22320000.0000
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: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.914

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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 RT, A-CHAIN
分子量 formula_weight	62768.7 kDa
EC 编号 ec_number	2.7.7.49
突变 mutation	L103N
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	7814

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIG

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 RT, B-CHAIN
分子量 formula_weight	51384.0 kDa
EC 编号 ec_number	2.7.7.49
突变 mutation	L103N
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

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETF

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	11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE
分子量 formula_weight	266.3 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	d1fkpa1
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	d1fkpa2
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	d1fkpb_
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	1fkpA01
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	1fkpA02
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	1fkpA03
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	1fkpA04
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	1fkpA05
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	1fkpB01
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	1fkpB02
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	1fkpB03
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	1fkpB04
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 (14)

Structural basis for the resilience of efavirenz (DMP-266) to drug resistance mutations in HIV-1 reverse transcriptase.

Structure Fold.Des. (2000)

PMID: 11080630 · DOI: 10.1016/S0969-2126(00)00513-X PRIMARY

;Binding of the second generattion non-nucleoside inhibitor S-1153 to HIV-1 reverse transcriptase involves extensive main chain hydrogen bonding ;

J.Biol.Chem. (2000)

DOI: 10.1074/jbc.275.19.14316

;Phenethylthiazolylthiourea (PETT) non-nucleoside inhibitors of HIV-1 and HIV-2 reverse transcriptases: structural and biochemical analyses ;

J.Biol.Chem. (2000)

DOI: 10.1074/jbc.275.8.5633

;Crystallographic analysis of the binding modes of non-nucleoside thiazoloisoindolinone inhibitors to HIV-1 reverse transcriptase and comparison with modeling studies ;

J.Med.Chem. (1999)

DOI: 10.1021/jm990275t

Design of MKC-442 (emivirine) analogues with improved activity against drug-resistant HIV mutants

J.Med.Chem. (1999)

DOI: 10.1021/jm990192c

Crystal structures of reverse transcriptase in complex with carboxanilide derivatives

Biochemistry (1998)

DOI: 10.1021/bi981309m

;3'-azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes ;

Proc.Natl.Acad.Sci.USA (1998)

DOI: 10.1073/pnas.95.16.9518

Continuous and discontinuous changes in the unit cell of HIV-1 reverse transcriptase crystals on dehydration

Acta Crystallogr.,Sect.D (1998)

DOI: 10.1107/S0907444998004284

;Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (BHAP) U-90152 explain resistance mutations for this non-nucleoside inhibitor ;

Proc.Natl.Acad.Sci.USA (1997)

DOI: 10.1073/pnas.94.8.3984

;Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors ;

J.Med.Chem. (1996)

DOI: 10.1021/jm960056x

The structure of HIV-1 reverse transcriptase complexed with 9-chloro-TIBO: lessons for inhibitor design

Structure (1995)

High Resolution Structures of HIV-1 RT From Four RT-inhibitor Complexes

Nat.Struct.Biol. (1995)

Mechanism of Inhibition of HIV-1 Reverse Transcriptase by Non-nucleoside Inhibitors

Nat.Struct.Biol. (1995)

Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 Angstrom Resolution

J.Mol.Biol. (1994)

DOI: 10.1006/jmbi.1994.1604

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晶胞边长 a length_a	139.700 Å
晶胞边长 b length_b	109.800 Å
晶胞边长 c length_c	72.900 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	4

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	2.900 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2090
R_work r_work	0.2150
R_free r_free	0.2810

fit	/app/data/saxs_computation/fk/1fkp/1fkp.fit
pddf	/app/data/pr_computation/fk/1fkp/1fkp.pr.out
profile	/app/data/saxs_computation/fk/1fkp/1fkp.dat

CRYSTAL STRUCTURE OF NNRTI RESISTANT K103N MUTANT HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE

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 (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 (14)

8. 文件与曲线 (10)

Files (7)

Curves (3)