3klh

Crystal structure of AZT-Resistant HIV-1 Reverse Transcriptase crosslinked to post-translocation AZTMP-Terminated DNA (COMPLEX P)

Method: X-RAY DIFFRACTION

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

Reverse transcriptase/ribonuclease H

Human immunodeficiency virus type 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	monoclonal antibody, heavy chain × 1 monoclonal antibody, light chain × 1 ;DNA (5'-D(APTGPCPTPAPGPGPCPGPCPCPCPGPAPAPCPAPGPGPGPAPCPTPGPTPG)-3') ; × 1 ;DNA (5'-D(APCPAPGPTPCPCPCPTPGPTPTPCPGPGP(MRG)PCPGPCPCP(ATM))-3') ; × 1 MAGNESIUM ION × 1 water × 6	Consistent with all polymers

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 3–564； UniProt 600–1161 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	3klh
Deposition date deposition_date	2009-11-07
Structure title title	Crystal structure of AZT-Resistant HIV-1 Reverse Transcriptase crosslinked to post-translocation AZTMP-Terminated DNA (COMPLEX P)
Keywords keywords	;HIV-1, REVERSE TRANSCRIPTASE, RT, AZT, AZT EXCISION, AZT RESISTANCE, RESISTANCE MECHANISM, AZT RESISTANCE MUTATIONS, P51/P66, NUCLEOSIDE INHIBITOR, AIDS, HIV, DNA POLYMERASE, NRTI, NUCLEOTIDE EXCISION, DNA-DIRECTED DNA POLYMERASE, MAGNESIUM, METAL-BINDING, MULTIFUNCTIONAL ENZYME, NUCLEASE, RNA-DIRECTED DNA POLYMERASE, TRANSFERASE, TRANSFERASE-DNA COMPLEX ;; 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.

3klh__assembly_1__model_1

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

Download this curve (.dat)

3klh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3klh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.43 Å
Rg (electron density)	44.48 Å
Total Rg	44.76 Å
Atom count	12334
Residues	1465
Excluded volume	217750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3klh__assembly_1__model_1`	hexameric （6）	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	Reverse transcriptase/ribonuclease H
Molecular weight formula_weight	64988.6 kDa
EC 编号 ec_number	2.7.7.49, 2.7.7.7, 3.1.26.4
Mutation mutation	M41L, D67N, K70R, T215Y, K219Q, C280S, Q258C
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	12472

MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTELEKEGKISKIGPENPYNTPVFAIKKKNSTRWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLYTPDQKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDICKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKILVL

Source Source

Source organism organism	Human immunodeficiency virus type 1
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11678
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	p51 RT
Molecular weight formula_weight	51120.6 kDa
Mutation mutation	C280S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQGGHHHHHHH

Source Source

Source organism organism	Human immunodeficiency virus type 1
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11678
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	monoclonal antibody, heavy chain
Molecular weight formula_weight	23362.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DIQMTQTTSSLSASLGDRVTISCSASQDISSYLNWYQQKPEGTVKLLIYYTSSLHSGVPSRFSGSGSGTDYSLTISNLEPEDIATYYCQQYSKFPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090

Entity 4 Entity 4 polymer

Description description	monoclonal antibody, light chain
Molecular weight formula_weight	24000.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

QITLKESGPGIVQPSQPFRLTCTFSGFSLSTSGIGVTWIRQPSGKGLEWLATIWWDDDNRYNPSLKSRLTVSKDTSNNQAFLNMMTVETADTAIYYCAQSAITSVTDSAMDHWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPADC

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090

Entity 5 Entity 5 polymer

Description description	;DNA (5'-D(APTGPCPTPAPGPGPCPGPCPCPCPGPAPAPCPAPGPGPGPAPCPTPGPTP*G)-3') ;
Molecular weight formula_weight	8367.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

ATGCTAGGCGCCCGAACAGGGACTGTG

Entity 6 Entity 6 polymer

Description description	;DNA (5'-D(APCPAPGPTPCPCPCPTPGPTPTPCPGPGP(MRG)PCPGPCPCP*(ATM))-3') ;
Molecular weight formula_weight	6490.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

ACAGTCCCTGTTCGGGCGCCT

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

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6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id	3klhA01
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	3klhA02
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	3klhA03
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	3klhA04
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	3klhA05
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	3klhB01
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	3klhB02
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	3klhB03
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	3klhB04
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	3klhC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3klhC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3klhD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3klhD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	166.472 Å
Unit-cell length b length_b	166.472 Å
Unit-cell length c length_c	220.822 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	6

Space group space_group	P 32 1 2
Space-group number int_tables_number	153
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	24.790 Å
R factor r_factor	0.2600
R_work r_work	0.2600
R_free r_free	0.2940

Crystal structure of AZT-Resistant HIV-1 Reverse Transcriptase crosslinked to post-translocation AZTMP-Terminated DNA (COMPLEX P)

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

3klh__assembly_1__model_1

3klh__assembly_1__model_1 | I(q)

3klh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

7. Citations (1)

Crystal structure of AZT-Resistant HIV-1 Reverse Transcriptase crosslinked to post-translocation AZTMP-Terminated DNA (COMPLEX P)

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

3klh__assembly_1__model_1

3klh__assembly_1__model_1 | I(q)

3klh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

7. Citations (1)