3qip

Structure of HIV-1 reverse transcriptase in complex with an RNase H inhibitor and nevirapine

Method: X-RAY DIFFRACTION

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

Reverse HIV-1 reverse transcriptase p66

HIV-1 M:B_HXB2R

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE × 1 MANGANESE (II) ION × 2 SULFATE ION × 2 CHLORIDE ION × 2 5,6-dihydroxy-2-[(2-phenyl-1H-indol-3-yl)methyl]pyrimidine-4-carboxylic acid × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE × 2 MANGANESE (II) ION × 4 SULFATE ION × 4 CHLORIDE ION × 4 5,6-dihydroxy-2-[(2-phenyl-1H-indol-3-yl)methyl]pyrimidine-4-carboxylic acid × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1H2
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–560； UniProt 588–1147 Author chain B； PDBConstruct 1–440； UniProt 588–1027

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	3qip
Deposition date deposition_date	2011-01-27
Structure title title	Structure of HIV-1 reverse transcriptase in complex with an RNase H inhibitor and nevirapine
Keywords keywords	HIV, reverse transcriptase, RNase H, polymerase, nuclease, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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.

3qip__assembly_1__model_1

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

Download this curve (.dat)

3qip__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3qip__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.33 Å
Rg (electron density)	34.48 Å
Total Rg	35.23 Å
Atom count	7899
Residues	956
Excluded volume	142130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3qip__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3qip__assembly_2__model_1`	tetrameric （4）	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 HIV-1 reverse transcriptase p66
Molecular weight formula_weight	64562.9 kDa
EC 编号 ec_number	3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13
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	8317

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVL

Source Source

Source organism organism	HIV-1 M:B_HXB2R
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11706
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	p51
Molecular weight formula_weight	51399.0 kDa
EC 编号 ec_number	3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

Source Source

Source organism organism	HIV-1 M:B_HXB2R
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11706
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE
Molecular weight formula_weight	266.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	5,6-dihydroxy-2-[(2-phenyl-1H-indol-3-yl)methyl]pyrimidine-4-carboxylic acid
Molecular weight formula_weight	361.4 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	418

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3qipa1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.2 — Reverse transcriptase

Domain ID domain_id	d3qipa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.1 — Ribonuclease H

Domain ID domain_id	d3qipb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.2 — Reverse transcriptase

CATH v4.4 (9 domains)

Domain ID domain_id	3qipA01
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	3qipA02
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	3qipA03
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	3qipA04
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	3qipA05
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	3qipB01
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	3qipB02
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	3qipB03
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	3qipB04
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	118.898 Å
Unit-cell length b length_b	154.876 Å
Unit-cell length c length_c	153.079 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.093 Å
Low-resolution limit resolution_low	47.354 Å
R factor r_factor	0.2188
R_work r_work	0.2163
R_free r_free	0.2669

Structure of HIV-1 reverse transcriptase in complex with an RNase H inhibitor and nevirapine

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

Reverse HIV-1 reverse transcriptase p66

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

3qip__assembly_1__model_1

3qip__assembly_1__model_1 | I(q)

3qip__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 non-polymer

Entity 4 Entity 4 non-polymer

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) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Structure of HIV-1 reverse transcriptase in complex with an RNase H inhibitor and nevirapine

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

Reverse HIV-1 reverse transcriptase p66

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

3qip__assembly_1__model_1

3qip__assembly_1__model_1 | I(q)

3qip__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 non-polymer

Entity 4 Entity 4 non-polymer

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) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)