SAXSdb — 3lp3

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

p15

Human immunodeficiency virus type 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1LW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–138； UniProt 1014–1149 Author chain B； PDBConstruct 3–138； UniProt 1014–1149

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	3lp3
Deposition date deposition_date	2010-02-04
Structure title title	p15 HIV RNaseH domain with inhibitor MK3
Keywords keywords	;Reverse Transcriptase, RNase H, HIV, AIDS, Capsid maturation, DNA integration, DNA-directed DNA polymerase, Endonuclease, Host cytoplasm, Host nucleus, Multifunctional enzyme, RNA-binding, RNA-directed DNA polymerase, Viral nucleoprotein, Virion, VIRAL PROTEIN ;; VIRAL PROTEIN
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.

3lp3__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3lp3__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lp3__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	15.38 Å
Rg (electron density)	14.12 Å
Total Rg	15.40 Å
Atom count	1042
Residues	131
Excluded volume	18685 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lp3__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3lp3__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3lp3__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	p15
Molecular weight formula_weight	15175.3 kDa
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	2104

GSYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKILFL

Source Source

Source organism organism	Human immunodeficiency virus type 1
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	3-[4-(diethylamino)phenoxy]-6-(ethoxycarbonyl)-5,8-dihydroxy-7-oxo-7,8-dihydro-1,8-naphthyridin-1-ium
Molecular weight formula_weight	413.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3lp3a_
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	d3lp3b_
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

CATH v4.4 (2 domains)

Domain ID domain_id	3lp3A00
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	3lp3B00
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	51.256 Å
Unit-cell length b length_b	51.256 Å
Unit-cell length c length_c	112.773 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 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	34.880 Å
R factor r_factor	0.2323
R_work r_work	0.2295
R_free r_free	0.2883

p15 HIV RNaseH domain with inhibitor MK3

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

p15

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

3lp3__assembly_2__model_1

3lp3__assembly_2__model_1 | I(q)

3lp3__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

p15 HIV RNaseH domain with inhibitor MK3

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

p15

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

3lp3__assembly_2__model_1

3lp3__assembly_2__model_1 | I(q)

3lp3__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)