1lwe

CRYSTAL STRUCTURE OF M41L/T215Y MUTANT HIV-1 REVERSE TRANSCRIPTASE (RTMN) IN COMPLEX WITH NEVIRAPINE

Method: X-RAY DIFFRACTION D_max: 116.7 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	1lwe
沉积日期 deposition_date	2002-05-31
结构标题 title	CRYSTAL STRUCTURE OF M41L/T215Y MUTANT HIV-1 REVERSE TRANSCRIPTASE (RTMN) IN COMPLEX WITH NEVIRAPINE
关键词 keywords	HIV-1 REVERSE TRANSCRIPTASE, AIDS, AZT, 3TC, NRTI, NEVIRAPINE, DRUG RESISTANCE MUTATIONS, 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	35.91 Å
回转半径 Rg (电子) rg_electron	35.19 Å
零角强度 I(0) i0	168397000.00
分子量 molecular_weight	109830.0 kDa
排除体积 excluded_volume	139910 Å³
包络体积 envelope_volume	194090 Å³
水化壳体积 shell_volume	46003 Å³
包络直径 envelope_diameter	122.5 Å
壳层 Rg shell_rg	41.79 Å
包络 Rg envelope_rg	34.53 Å
形状 Rg shape_rg	35.13 Å
总 Rg total_rg	35.91 Å
总原子数 total_atoms	7774
残基数 n_residues	943
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	116.7 Å
Rg (实空间) rg_real	35.82 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	1.6840e+08
I(0) 误差 (实空间) i0_real_error	2.4700e+06
Rg (倒空间) rg_reciprocal	35.88 Å
I(0) (倒空间) i0_reciprocal	168400000.0000
解质量估计 total_estimate	0.8991
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	45.1 Å
偏度 Skewness skewness	0.208
峰度 Kurtosis kurtosis	-0.499
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22880000.0000
实空间数据点数 n_real_points	45
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: 0.997; Smooth: 0.909

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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	HIV-1 REVERSE TRANSCRIPTASE
分子量 formula_weight	64639.0 kDa
EC 编号 ec_number	2.7.7.49
突变 mutation	M41L/T215Y
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	7793

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTELEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLYTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVL

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
分子量 formula_weight	51443.1 kDa
EC 编号 ec_number	2.7.7.49
突变 mutation	M41L/T215Y
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

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	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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

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	19

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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	d1lwea1
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	d1lwea2
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	d1lweb_
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	1lweA01
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	1lweA02
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	1lweA03
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	1lweA04
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	1lweA05
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	1lweB01
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	1lweB02
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	1lweB03
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	1lweB04
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 (17)

;Crystal structures of Zidovudine- or Lamivudine-resistant human immunodeficiency virus type 1 reverse transcriptases containing mutations at codons 41, 184, and 215. ;

J.Virol. (2002)

PMID: 12208978 · DOI: 10.1128/JVI.76.19.10015-10019.2002 PRIMARY

;Structural Mechanisms of Drug Resistance for Mutations at Codons 181 and 188 in HIV-1 Reverse Transcriptase and the Improved Resilience of Second Generation Non-Nucleoside Inhibitors ;

J.Mol.Biol. (2001)

DOI: 10.1006/jmbi.2001.4988

2-Amino-6-Arylsulfonylbenzonitriles as Non-Nucleoside reverse Transcriptase Inhibitors of HIV-1

J.Med.Chem. (2001)

DOI: 10.1021/jm0004906

Structural Basis for the Resilience of Efavirenz (Dmp-266) to Drug Resistance Mutations in HIV-1 Reverse Transcriptase

Structure (2000)

DOI: 10.1016/S0969-2126(00)00513-X

;Binding of the Second Generation 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 Thiazoloisoindolinone Non-Nucleoside 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

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

Crystal Structures of HIV-1 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

;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 A 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	111.300 Å
晶胞边长 c length_c	74.500 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	2.810 Å
最低分辨率 resolution_low	29.990 Å
R 因子 r_factor	—
R_work r_work	0.2130
R_free r_free	0.3020

fit	/app/data/saxs_computation/lw/1lwe/1lwe.fit
pddf	/app/data/pr_computation/lw/1lwe/1lwe.pr.out
profile	/app/data/saxs_computation/lw/1lwe/1lwe.dat

CRYSTAL STRUCTURE OF M41L/T215Y MUTANT HIV-1 REVERSE TRANSCRIPTASE (RTMN) 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 (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 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. 引用文献 (17)

8. 文件与曲线 (10)

Files (7)

Curves (3)