2ic3

Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcriptase (RT) in Complex with Nonnucleoside Inhibitor HBY 097

Method: X-RAY DIFFRACTION

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

Reverse transcriptase/ribonuclease H (p66 RT)

Human immunodeficiency virus type 1 BH10

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 1 (S)-4-ISOPROPOXYCARBONYL-6-METHOXY-3-METHYLTHIOMETHYL-3,4-DIHYDROQUINOXALIN-2(1H)-THIONE × 1 water × 1	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 1–560； UniProt 599–1158 Author chain B； PDBConstruct 1–447； UniProt 599–1045

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	2ic3
Deposition date deposition_date	2006-09-12
Structure title title	Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcriptase (RT) in Complex with Nonnucleoside Inhibitor HBY 097
Keywords keywords	RT, NNRTI, NONNUCLEOSIDE INHIBITOR, DRUG RESISTANCE, HIV, AIDS, DRUG DESIGN, 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.

2ic3__assembly_1__model_1

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

Download this curve (.dat)

2ic3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ic3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.56 Å
Rg (electron density)	34.78 Å
Total Rg	35.46 Å
Atom count	8000
Residues	985
Excluded volume	143930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ic3__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 (5)

Entity 1 Entity 1 polymer

Description description	Reverse transcriptase/ribonuclease H (p66 RT)
Molecular weight formula_weight	64425.9 kDa
EC 编号 ec_number	2.7.7.49
Mutation mutation	C280S
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	8002

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVICQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKIL

Source Source

Source organism organism	Human immunodeficiency virus type 1 BH10
NCBI taxonomy ID ncbi_taxonomy_id	11678
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Reverse transcriptase/ribonuclease H (p51 RT)
Molecular weight formula_weight	51970.6 kDa
EC 编号 ec_number	2.7.7.49
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

Source Source

Source organism organism	Human immunodeficiency virus type 1 BH10
NCBI taxonomy ID ncbi_taxonomy_id	11678
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(S)-4-ISOPROPOXYCARBONYL-6-METHOXY-3-METHYLTHIOMETHYL-3,4-DIHYDROQUINOXALIN-2(1H)-THIONE
Molecular weight formula_weight	340.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2ic3a1
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	d2ic3a2
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.55.3.0 — automated matches

Domain ID domain_id	d2ic3b_
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	2ic3A01
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	2ic3A02
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	2ic3A03
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	2ic3A04
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	2ic3A05
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	2ic3B01
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	2ic3B02
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	2ic3B03
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	2ic3B04
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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7. Citations (6)

;Crystal Structures of Clinically Relevant Lys103Asn/Tyr181Cys Double Mutant HIV-1 Reverse Transcriptase in Complexes with ATP and Non-nucleoside Inhibitor HBY 097. ;

J.Mol.Biol. (2007)

PMID: 17056061 · DOI: 10.1016/j.jmb.2006.08.097 PRIMARY

;Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants. ;

J.Med.Chem. (2004)

PMID: 15115397 · DOI: 10.1021/jm030558s

The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance.

J.Mol.Biol. (2001)

PMID: 11371163 · DOI: 10.1006/jmbi.2001.4648

;Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance. ;

J.Mol.Biol. (1998)

PMID: 9813120 · DOI: 10.1006/jmbi.1998.2171

;Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A Resolution: Implications of Conformational Changes for Polymerization and Inhibition Mechanisms ;

Structure (1996)

PMID: 8805568 · DOI: 10.1016/S0969-2126(96)00091-3

;Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant. ;

J.Mol.Biol. (1996)

PMID: 9000632 · DOI: 10.1006/jmbi.1996.0698

Unit-cell length a length_a	223.210 Å
Unit-cell length b length_b	67.610 Å
Unit-cell length c length_c	103.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.39 °
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	3.000 Å
Low-resolution limit resolution_low	19.900 Å
R factor r_factor	—
R_work r_work	0.2570
R_free r_free	0.3100

Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcriptase (RT) in Complex with Nonnucleoside Inhibitor HBY 097

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

Reverse transcriptase/ribonuclease H (p66 RT)

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

2ic3__assembly_1__model_1

2ic3__assembly_1__model_1 | I(q)

2ic3__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (6)

Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcriptase (RT) in Complex with Nonnucleoside Inhibitor HBY 097

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

Reverse transcriptase/ribonuclease H (p66 RT)

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

2ic3__assembly_1__model_1

2ic3__assembly_1__model_1 | I(q)

2ic3__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (6)