← Back to search
2i60

Crystal structure of [Phe23]M47, 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
▼

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

EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)

Human immunodeficiency virus 1

UniProt P35961

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 [PHE23]M47, SCORPION-TOXIN MIMIC OF CD4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 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 [PHE23]M47, 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

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1g9n 1yyl 1yyl 1yym 1yym 2i5y 2i5y 2i60 2i60 2qad 2qad 2qad

16 assemblies; showing the first 12

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2i60
Deposition date deposition_date2006-08-26
Structure title titleCrystal structure of [Phe23]M47, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 GP120 envelope glycoprotein and anti-HIV-1 antibody 17B
Keywords keywordsHIV-1, GP120, YU2, scorpion toxin, CD4 mimic, [Phe23]M47, antibody, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
▼

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.

2i60__assembly_1__model_1

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

Download this curve (.dat)

2i60__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2i60__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）37.76 Å
Rg (electron density)38.41 Å
Total Rg38.55 Å
Atom count5975
Residues760
Excluded volume106030 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2i60__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2i60__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

▼

6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (13 domains)

Domain ID domain_idd2i60g_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.172 — gp120 core
Superfamily Superfamily superfamilyd.172.1 — gp120 core
Family Family familyd.172.1.1 — gp120 core
Domain ID domain_idd2i60h1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2i60h2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2i60l1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2i60l2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2i60m1
Class classk — Designed proteins
Fold Fold foldk.23 — Scorpion toxin-based designs
Superfamily Superfamily superfamilyk.23.1 — Scorpion toxin-based designs
Family Family familyk.23.1.2 — Mini-protein reproducing the core of the CD4 surface
Domain ID domain_idd2i60p2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.172 — gp120 core
Superfamily Superfamily superfamilyd.172.1 — gp120 core
Family Family familyd.172.1.1 — gp120 core
Domain ID domain_idd2i60p3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2i60q1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2i60q2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2i60r1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2i60r2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2i60s1
Class classk — Designed proteins
Fold Fold foldk.23 — Scorpion toxin-based designs
Superfamily Superfamily superfamilyk.23.1 — Scorpion toxin-based designs
Family Family familyk.23.1.2 — Mini-protein reproducing the core of the CD4 surface

CATH v4.4 (10 domains)

Domain ID domain_id2i60G00
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology40 — HIV Envelope Protein Gp120; Chain G
Homologous superfamily homologous superfamily20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein
Domain ID domain_id2i60H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i60H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i60L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i60L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i60P00
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology40 — HIV Envelope Protein Gp120; Chain G
Homologous superfamily homologous superfamily20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein
Domain ID domain_id2i60Q01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i60Q02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i60R01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2i60R02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
▶

7. Citations (1)