1yym

crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b

Method: X-RAY DIFFRACTION

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

Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120)

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	antibody 17b light chain × 1 antibody 17b heavy chain × 1 F23, scorpion-toxin mimic of CD4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 1,2-ETHANEDIOL × 2 ISOPROPYL ALCOHOL × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	antibody 17b light chain × 1 antibody 17b heavy chain × 1 F23, scorpion-toxin mimic of CD4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ISOPROPYL ALCOHOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENV_HV1Y2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 5–49； UniProt 82–126 Author chain G； PDBConstruct 53–155； UniProt 191–293 Author chain G； PDBConstruct 159–313； UniProt 325–479 Author chain P； PDBConstruct 5–49； UniProt 82–126 Author chain P； PDBConstruct 53–155； UniProt 191–293 Author chain P； PDBConstruct 159–313； UniProt 325–479

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	1yym
Deposition date deposition_date	2005-02-25
Structure title title	crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b
Keywords keywords	HIV-1, gp120, YU2, scorpion toxin, CD4 mimic, F23, antibody, Viral protein-Immune system COMPLEX; Viral protein/Immune system
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.

1yym__assembly_1__model_1

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

Download this curve (.dat)

1yym__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yym__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.86 Å
Rg (electron density)	38.50 Å
Total Rg	38.65 Å
Atom count	6029
Residues	769
Excluded volume	106960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yym__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yym__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	Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120)
Molecular weight formula_weight	34838.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,P
Atom count atom_count	12823

GARSEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGAGHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	antibody 17b light chain
Molecular weight formula_weight	23399.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,Q

DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	antibody 17b heavy chain
Molecular weight formula_weight	24457.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,R

EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Mus musculus

Entity 4 Entity 4 polymer

Description description	F23, scorpion-toxin mimic of CD4
Molecular weight formula_weight	2863.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,S

XNLHFCQLRCKSLGLLGKCAGSFCACX

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	16

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	789

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6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1yymg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.172 — gp120 core
Superfamily Superfamily superfamily	d.172.1 — gp120 core
Family Family family	d.172.1.1 — gp120 core

Domain ID domain_id	d1yymh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1yymh2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1yyml1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1yyml2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1yymm1
Class class	k — Designed proteins
Fold Fold fold	k.23 — Scorpion toxin-based designs
Superfamily Superfamily superfamily	k.23.1 — Scorpion toxin-based designs
Family Family family	k.23.1.2 — Mini-protein reproducing the core of the CD4 surface

Domain ID domain_id	d1yymp_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.172 — gp120 core
Superfamily Superfamily superfamily	d.172.1 — gp120 core
Family Family family	d.172.1.1 — gp120 core

Domain ID domain_id	d1yymq1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1yymq2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1yymr1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1yymr2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1yyms1
Class class	k — Designed proteins
Fold Fold fold	k.23 — Scorpion toxin-based designs
Superfamily Superfamily superfamily	k.23.1 — Scorpion toxin-based designs
Family Family family	k.23.1.2 — Mini-protein reproducing the core of the CD4 surface

CATH v4.4 (10 domains)

Domain ID domain_id	1yymG00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	40 — HIV Envelope Protein Gp120; Chain G
Homologous superfamily homologous superfamily	20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein

Domain ID domain_id	1yymH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yymH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yymL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yymL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yymP00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	40 — HIV Envelope Protein Gp120; Chain G
Homologous superfamily homologous superfamily	20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein

Domain ID domain_id	1yymQ01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yymQ02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yymR01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yymR02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	51.620 Å
Unit-cell length b length_b	157.041 Å
Unit-cell length c length_c	108.929 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2680

crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b

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

Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120)

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

1yym__assembly_1__model_1

1yym__assembly_1__model_1 | I(q)

1yym__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer 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) 22 domains

SCOP 2.08 (12 domains)

CATH v4.4 (10 domains)

7. Citations (1)

crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b

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

Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120)

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

1yym__assembly_1__model_1

1yym__assembly_1__model_1 | I(q)

1yym__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer 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) 22 domains

SCOP 2.08 (12 domains)

CATH v4.4 (10 domains)

7. Citations (1)