SAXSdb — 3ao1

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

POL polyprotein

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CADMIUM ION × 4 SULFATE ION × 1 1,3-benzodioxol-5-ol × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q72498_9HIV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–163； UniProt 765–927 Author chain B； PDBConstruct 1–163； UniProt 765–927

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	3ao1
Deposition date deposition_date	2010-09-17
Structure title title	Fragment-based approach to the design of ligands targeting a novel site in HIV-1 integrase
Keywords keywords	;DNA INTEGRATION, AIDS, INTEGRASE, ENDONUCLEASE, POLYNUCLEOTIDYL TRANSFERASE, DNA BINDING, VIRAL PROTEIN, RNaseH, Fragment binding, VIRAL PROTEIN-TRANSFERASE INHIBITOR complex ;; VIRAL PROTEIN/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.

3ao1__assembly_1__model_1

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

Download this curve (.dat)

3ao1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ao1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.16 Å
Rg (electron density)	17.82 Å
Total Rg	18.93 Å
Atom count	2198
Residues	283
Excluded volume	39292 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ao1__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	POL polyprotein
Molecular weight formula_weight	17802.2 kDa
Mutation mutation	C56S, W131D, F139D, F185H
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2270

MHGQVDSSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACDWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGGIGGYSAGERIVDIIATDIQTKE

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,3-benzodioxol-5-ol
Molecular weight formula_weight	138.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	72

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ao1a_
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.55.3.2 — Retroviral integrase, catalytic domain

Domain ID domain_id	d3ao1b_
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.55.3.2 — Retroviral integrase, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id	3ao1A00
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	3ao1B00
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

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Unit-cell length a length_a	60.587 Å
Unit-cell length b length_b	61.997 Å
Unit-cell length c length_c	81.765 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	49.400 Å
R factor r_factor	0.2188
R_work r_work	0.2163
R_free r_free	0.2676

Fragment-based approach to the design of ligands targeting a novel site in HIV-1 integrase

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

POL polyprotein

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

3ao1__assembly_1__model_1

3ao1__assembly_1__model_1 | I(q)

3ao1__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Fragment-based approach to the design of ligands targeting a novel site in HIV-1 integrase

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

POL polyprotein

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

3ao1__assembly_1__model_1

3ao1__assembly_1__model_1 | I(q)

3ao1__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)