6kdk

HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dCTP ternary complex

Method: X-RAY DIFFRACTION

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

HIV-1 reverse transcriptase p66 subunit

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 其他Polymer 1	HIV-1 RT p51 subunit × 1 （P12497） DNA/RNA (38-MER) × 1 beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 GLYCEROL × 2 water × 3	Review required
2	Protein–DNA	Heteromer	Protein 2 DNA 1	HIV-1 RT p51 subunit × 1 （P12497） DNA/RNA (38-MER) × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 GLYCEROL × 2 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 type 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 其他Polymer 1	HIV-1 reverse transcriptase p66 subunit × 1 （D3XFN5） DNA/RNA (38-MER) × 1 beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 GLYCEROL × 2 water × 3	Review required
2	Protein–DNA	Heteromer	Protein 2 DNA 1	HIV-1 reverse transcriptase p66 subunit × 1 （D3XFN5） DNA/RNA (38-MER) × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 GLYCEROL × 2 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	6kdk
Deposition date deposition_date	2019-07-02
Structure title title	HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dCTP ternary complex
Keywords keywords	dCTP, HIV-1, HBV, reverse transcriptase, drug resistance, drug sensitivity, TRANSFERASE-DNA complex, REPLICATION; TRANSFERASE/DNA
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.

6kdk__assembly_1__model_1

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

Download this curve (.dat)

6kdk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6kdk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.07 Å
Rg (electron density)	32.85 Å
Total Rg	33.44 Å
Atom count	8630
Residues	992
Excluded volume	152760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6kdk__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6kdk__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 (8)

Entity 1 Entity 1 polymer

Description description	HIV-1 reverse transcriptase p66 subunit
Molecular weight formula_weight	64033.4 kDa
Mutation mutation	Q214M, Y215F, F250Y, C261S, C379S
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	17528

MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKQKKSVTVLDVGDAFYSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPMGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYAGIKVRQLSKLLRGTKALTEVVPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMKGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIIGAETFYVDGAANRETKLGKAGYVTDRGRQKVVPLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG

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	C749S, C867S
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 type 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	11764.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F

TAATGCCCCCCCTTCGGTGCTTTGCACCGAAGGGGGGG

Entity 4 Entity 4 branched

Description description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	467.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	232

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	6kdkA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	10 — HIV Type 1 Reverse Transcriptase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — HIV Type 1 Reverse Transcriptase, subunit A, domain 1

Domain ID domain_id	6kdkA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkA05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	6kdkB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	10 — HIV Type 1 Reverse Transcriptase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — HIV Type 1 Reverse Transcriptase, subunit A, domain 1

Domain ID domain_id	6kdkB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	10 — HIV Type 1 Reverse Transcriptase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — HIV Type 1 Reverse Transcriptase, subunit A, domain 1

Domain ID domain_id	6kdkC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkC04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkC05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	6kdkD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	10 — HIV Type 1 Reverse Transcriptase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — HIV Type 1 Reverse Transcriptase, subunit A, domain 1

Domain ID domain_id	6kdkD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkD03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	6kdkD04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

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Unit-cell length a length_a	284.852 Å
Unit-cell length b length_b	284.852 Å
Unit-cell length c length_c	95.926 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	2.560 Å
Low-resolution limit resolution_low	48.743 Å
R factor r_factor	0.1922
R_work r_work	0.1900
R_free r_free	0.2342

HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dCTP ternary complex

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

HIV-1 reverse transcriptase p66 subunit

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

6kdk__assembly_1__model_1

6kdk__assembly_1__model_1 | I(q)

6kdk__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 (8)

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 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)

HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dCTP ternary complex

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

HIV-1 reverse transcriptase p66 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

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

6kdk__assembly_1__model_1

6kdk__assembly_1__model_1 | I(q)

6kdk__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 (8)

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 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)