5hfm

Gp41-targeting HIV-1 fusion inhibitors with hook-like Ile-Asp-Leu tail

Method: X-RAY DIFFRACTION

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

Envelope glycoprotein gp160,gp41 CHR region

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 3	TRIS(HYDROXYETHYL)AMINOMETHANE × 1 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	TRIS(HYDROXYETHYL)AMINOMETHANE × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENV_HV1LW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–47； UniProt 539–581 Author chain B； PDBConstruct 5–47； UniProt 539–581 Author chain C； PDBConstruct 5–47； UniProt 539–581 Author chain D； PDBConstruct 5–47； UniProt 539–581 Author chain E； PDBConstruct 5–47； UniProt 539–581 Author chain F； PDBConstruct 5–47； UniProt 539–581

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	5hfm
Deposition date deposition_date	2016-01-07
Structure title title	Gp41-targeting HIV-1 fusion inhibitors with hook-like Ile-Asp-Leu tail
Keywords keywords	HIV-1 fusion inhibitor, Ile-Asp-Leu tail, hook-like tail, 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.

5hfm__assembly_1__model_1

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

Download this curve (.dat)

5hfm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5hfm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.34 Å
Rg (electron density)	19.38 Å
Total Rg	20.40 Å
Atom count	1899
Residues	229
Excluded volume	33955 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5hfm__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5hfm__assembly_2__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein gp160,gp41 CHR region
Molecular weight formula_weight	9446.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	3940

GPMAVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILSGGRGGWEEWDKKIEEYTKKIEELIKKSQNQQIDL

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	TRIS(HYDROXYETHYL)AMINOMETHANE
Molecular weight formula_weight	163.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d5hfma1
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.2 — Virus ectodomain
Family Family family	h.3.2.1 — Virus ectodomain

Domain ID domain_id	d5hfma2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5hfmb1
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.2 — Virus ectodomain
Family Family family	h.3.2.1 — Virus ectodomain

Domain ID domain_id	d5hfmb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5hfmc1
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.2 — Virus ectodomain
Family Family family	h.3.2.1 — Virus ectodomain

Domain ID domain_id	d5hfmc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5hfmd1
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.2 — Virus ectodomain
Family Family family	h.3.2.1 — Virus ectodomain

Domain ID domain_id	d5hfmd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5hfme1
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.2 — Virus ectodomain
Family Family family	h.3.2.1 — Virus ectodomain

Domain ID domain_id	d5hfme2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5hfmf1
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.2 — Virus ectodomain
Family Family family	h.3.2.1 — Virus ectodomain

Domain ID domain_id	d5hfmf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	5hfmA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	5hfmB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	5hfmC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	5hfmD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	5hfmE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	5hfmF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

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Unit-cell length a length_a	39.112 Å
Unit-cell length b length_b	39.076 Å
Unit-cell length c length_c	90.602 Å
Unit-cell angle α angle_alpha	90.03 °
Unit-cell angle β angle_beta	89.98 °
Unit-cell angle γ angle_gamma	120.06 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.298 Å
Low-resolution limit resolution_low	33.850 Å
R factor r_factor	0.2029
R_work r_work	0.2003
R_free r_free	0.2467

Gp41-targeting HIV-1 fusion inhibitors with hook-like Ile-Asp-Leu tail

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

Envelope glycoprotein gp160,gp41 CHR region

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

5hfm__assembly_1__model_1

5hfm__assembly_1__model_1 | I(q)

5hfm__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Gp41-targeting HIV-1 fusion inhibitors with hook-like Ile-Asp-Leu tail

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

Envelope glycoprotein gp160,gp41 CHR region

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

5hfm__assembly_1__model_1

5hfm__assembly_1__model_1 | I(q)

5hfm__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)