SAXSdb — 8u6o

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Reverse transcriptase/ribonuclease H

Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	5-{2-[3-oxo-3-(pyrrolidin-1-yl)propoxy]phenoxy}naphthalene-2-carbonitrile × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1B1
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 3–556； UniProt 600–1153 Author chain B； PDBConstruct 1–428； UniProt 600–1027

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8u6o
Deposition date deposition_date	2023-09-13
Last revision last_revision	2023-11-08
Structure title title	Crystal Structure of HIV-1 Reverse Transcriptase in Complex with5-(2-(3-oxo-3-(pyrrolidin-1-yl)propoxy)phenoxy)-2-naphthonitrile (JLJ753), a non-nucleoside inhibitor
Keywords keywords	REVERSE TRANSCRIPTASE, ANTIVIRAL, DRUG DESIGN, HIV-1, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8u6o__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8u6o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8u6o__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	35.15 Å
Rg (electron density)	34.30 Å
Total Rg	34.90 Å
Atom count	7513
Residues	957
Excluded volume	134360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8u6o__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Reverse transcriptase/ribonuclease H
Molecular weight formula_weight	63932.2 kDa
EC 编号 ec_number	2.7.7.49,2.7.7.7,3.1.26.13
Mutation mutation	C879S, K172A, K173A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7538

MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA

Source Source

Source organism organism	Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
NCBI taxonomy ID ncbi_taxonomy_id	11678
Host organism host_organism	Human immunodeficiency virus 1

Entity 2 Entity 2 polymer

Description description	p51 RT
Molecular weight formula_weight	50039.5 kDa
Mutation mutation	C879S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQ

Source Source

Source organism organism	Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
NCBI taxonomy ID ncbi_taxonomy_id	11678
Host organism host_organism	Human immunodeficiency virus 1

Entity 3 Entity 3 non-polymer

Description description	5-{2-[3-oxo-3-(pyrrolidin-1-yl)propoxy]phenoxy}naphthalene-2-carbonitrile
Molecular weight formula_weight	386.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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Unit-cell length a length_a	224.188 Å
Unit-cell length b length_b	68.031 Å
Unit-cell length c length_c	103.803 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.480 Å
Low-resolution limit resolution_low	43.450 Å
R factor r_factor	0.2275
R_work r_work	0.2259
R_free r_free	0.2688

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with5-(2-(3-oxo-3-(pyrrolidin-1-yl)propoxy)phenoxy)-2-naphthonitrile (JLJ753), a non-nucleoside inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Reverse transcriptase/ribonuclease H

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8u6o__assembly_1__model_1

8u6o__assembly_1__model_1 | I(q)

8u6o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with5-(2-(3-oxo-3-(pyrrolidin-1-yl)propoxy)phenoxy)-2-naphthonitrile (JLJ753), a non-nucleoside inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Reverse transcriptase/ribonuclease H

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8u6o__assembly_1__model_1

8u6o__assembly_1__model_1 | I(q)

8u6o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)