8x21

HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:ETV-TP ternary complex

Method: X-RAY DIFFRACTION

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

Pol protein (Fragment)

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 1	HIV-1 RT p51 subunit × 1 （P12497） DNA/RNA (38-MER) × 1 ;[[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate ; × 1 MAGNESIUM ION × 1 GLYCEROL × 3 water × 3	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 2 DNA 1	HIV-1 RT p51 subunit × 1 （P12497） DNA/RNA (38-MER) × 1 ;[[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate ; × 1 MAGNESIUM ION × 1 GLYCEROL × 3 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3XFN5_9HIV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–557； UniProt 100–654 Author chain C； PDBConstruct 3–557； UniProt 100–654

HIV-1 RT p51 subunit

Human immunodeficiency virus 1

UniProt P12497

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 1	Pol protein (Fragment) × 1 （D3XFN5） DNA/RNA (38-MER) × 1 ;[[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate ; × 1 MAGNESIUM ION × 1 GLYCEROL × 3 water × 3	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 2 DNA 1	Pol protein (Fragment) × 1 （D3XFN5） DNA/RNA (38-MER) × 1 ;[[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate ; × 1 MAGNESIUM ION × 1 GLYCEROL × 3 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1N5
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 17–444； UniProt 588–1015 Author chain D； PDBConstruct 17–444； UniProt 588–1015

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	8x21
Deposition date deposition_date	2023-11-09
Last revision last_revision	2024-07-17
Structure title title	HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:ETV-TP ternary complex
Keywords keywords	reverse transcriptase, HIV-1, HBV, drug resistance, nucleoside analogue, entecavir, TRANSFERASE; TRANSFERASE
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.

8x21__assembly_1__model_1

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

Download this curve (.dat)

8x21__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8x21__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.04 Å
Rg (electron density)	32.80 Å
Total Rg	33.40 Å
Atom count	8613
Residues	992
Excluded volume	152470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8x21__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8x21__assembly_2__model_1`	trimeric （3）	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 (7)

Entity 1 Entity 1 polymer

Description description	Pol protein (Fragment)
Molecular weight formula_weight	64019.4 kDa
Mutation mutation	L74V, Y115F, F116Y, Q151M, C162S, C280S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	17751

MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKVVDFRELNKRTQDFWEVQLGIPHPAGLKQKKSVTVLDVGDAFYSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPMGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYAGIKVRQLSKLLRGTKALTEVVPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMKGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIIGAETFYVDGAANRETKLGKAGYVTDRGRQKVVPLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	HIV-1 RT p51 subunit
Molecular weight formula_weight	51861.5 kDa
Mutation mutation	C162S, C280S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MAHHHHHHALEVLFQGPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKQKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYAGIKVRQLSKLLRGTKALTEVVPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMKGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPPLVKLWYQ

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	DNA/RNA (38-MER)
Molecular weight formula_weight	11724.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F

TAATCGCCCCCCTTCGGTGCTTTGCACCGAAGGGGGGC

Entity 4 Entity 4 non-polymer

Description description	;[[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate ;
Molecular weight formula_weight	517.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	458

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Unit-cell length a length_a	284.447 Å
Unit-cell length b length_b	284.447 Å
Unit-cell length c length_c	95.728 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.330 Å
Low-resolution limit resolution_low	48.666 Å
R factor r_factor	0.1775
R_work r_work	0.1754
R_free r_free	0.2181

HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:ETV-TP ternary complex

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

Pol protein (Fragment)

State in the Current Structure

Other States of the Same Protein in the Database

HIV-1 RT p51 subunit

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

8x21__assembly_1__model_1

8x21__assembly_1__model_1 | I(q)

8x21__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:ETV-TP ternary complex

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

Pol protein (Fragment)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HIV-1 RT p51 subunit

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

8x21__assembly_1__model_1

8x21__assembly_1__model_1 | I(q)

8x21__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)