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2qad

Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein gp160

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 T-cell surface glycoprotein CD4 × 1 （P01730） anti-HIV-1 antibody 412d light chain × 1 （Q6GMX8） anti-HIV-1 antibody 412d heavy chain × 1 （A4F255） 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 MALONIC ACID × 2 1,2-ETHANEDIOL × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 T-cell surface glycoprotein CD4 × 1 （P01730） anti-HIV-1 antibody 412d light chain × 1 （Q6GMX8） anti-HIV-1 antibody 412d heavy chain × 1 （A4F255） 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 MALONIC ACID × 2 1,2-ETHANEDIOL × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 8 T-cell surface glycoprotein CD4 × 2 （P01730） anti-HIV-1 antibody 412d light chain × 2 （Q6GMX8） anti-HIV-1 antibody 412d heavy chain × 2 （A4F255） 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 MALONIC ACID × 4 1,2-ETHANEDIOL × 7 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 A； PDBConstruct 1–33； UniProt 88–120 Author chain A； PDBConstruct 38–322； UniProt 195–479 Author chain E； PDBConstruct 1–33； UniProt 88–120 Author chain E； PDBConstruct 38–322； UniProt 195–479

T-cell surface glycoprotein CD4

Homo sapiens

UniProt P01730

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Envelope glycoprotein gp160 × 1 （P35961） anti-HIV-1 antibody 412d light chain × 1 （Q6GMX8） anti-HIV-1 antibody 412d heavy chain × 1 （A4F255） 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 MALONIC ACID × 2 1,2-ETHANEDIOL × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Envelope glycoprotein gp160 × 1 （P35961） anti-HIV-1 antibody 412d light chain × 1 （Q6GMX8） anti-HIV-1 antibody 412d heavy chain × 1 （A4F255） 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 MALONIC ACID × 2 1,2-ETHANEDIOL × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 8 Envelope glycoprotein gp160 × 2 （P35961） anti-HIV-1 antibody 412d light chain × 2 （Q6GMX8） anti-HIV-1 antibody 412d heavy chain × 2 （A4F255） 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 MALONIC ACID × 4 1,2-ETHANEDIOL × 7 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1cdj 1cdu 1cdy 1wbr 1wio 1wio 1wip 1wip 1wiq 1wiq 2klu

11 assemblies

Homodimer
1cdh 1cdi 3cd4

3 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1g9m 1g9n 1gc1 1jl4 1q68 1rzj 1rzk 2b4c 2b4c 2nxy 2nxz 2ny0

86 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CD4_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–181； UniProt 26–206 Author chain F； PDBConstruct 1–181； UniProt 26–206

anti-HIV-1 antibody 412d light chain

Homo sapiens

UniProt Q6GMX8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Envelope glycoprotein gp160 × 1 （P35961） T-cell surface glycoprotein CD4 × 1 （P01730） anti-HIV-1 antibody 412d heavy chain × 1 （A4F255） 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 MALONIC ACID × 2 1,2-ETHANEDIOL × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Envelope glycoprotein gp160 × 1 （P35961） T-cell surface glycoprotein CD4 × 1 （P01730） anti-HIV-1 antibody 412d heavy chain × 1 （A4F255） 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 MALONIC ACID × 2 1,2-ETHANEDIOL × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 8 Envelope glycoprotein gp160 × 2 （P35961） T-cell surface glycoprotein CD4 × 2 （P01730） anti-HIV-1 antibody 412d heavy chain × 2 （A4F255） 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 MALONIC ACID × 4 1,2-ETHANEDIOL × 7 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
2fjf 2fjf 2fjf 2fjf 2fjf 2fjf 2fjf 2fjf 2fjf 2fjf 2fjf 2fjf

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q6GMX8_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–214； UniProt 23–236 Author chain G； PDBConstruct 1–214； UniProt 23–236

anti-HIV-1 antibody 412d heavy chain

Homo sapiens

UniProt A4F255

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Envelope glycoprotein gp160 × 1 （P35961） T-cell surface glycoprotein CD4 × 1 （P01730） anti-HIV-1 antibody 412d light chain × 1 （Q6GMX8） 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 MALONIC ACID × 2 1,2-ETHANEDIOL × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Envelope glycoprotein gp160 × 1 （P35961） T-cell surface glycoprotein CD4 × 1 （P01730） anti-HIV-1 antibody 412d light chain × 1 （Q6GMX8） 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 MALONIC ACID × 2 1,2-ETHANEDIOL × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 8 Envelope glycoprotein gp160 × 2 （P35961） T-cell surface glycoprotein CD4 × 2 （P01730） anti-HIV-1 antibody 412d light chain × 2 （Q6GMX8） 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 MALONIC ACID × 4 1,2-ETHANEDIOL × 7 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
2qad 2qad 2qad 8fk5

4 assemblies

View Construct and Data Evidence
UniProt name A4F255_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 36–231； UniProt 33–228 Author chain H； PDBConstruct 36–231； UniProt 33–228

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_id2qad
Deposition date deposition_date2007-06-14
Structure title titleStructure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4
Keywords keywordsviral protein/immune system, viral protein-immune system complex; viral protein/immune system
Experimental Method methodX-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.

2qad__assembly_1__model_1

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

Download this curve (.dat)

2qad__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.

2qad__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）39.64 Å
Rg (electron density)39.71 Å
Total Rg40.02 Å
Atom count7524
Residues939
Excluded volume133400 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2qad__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2qad__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2qad__assembly_3__model_1 octameric （8） 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 (7)

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6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2qadb1
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_idd2qadb2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.3 — C2 set domains
Domain ID domain_idd2qadd1
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_idd2qadd2
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_idd2qadf1
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_idd2qadf2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.3 — C2 set domains
Domain ID domain_idd2qadh1
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_idd2qadh2
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)

CATH v4.4 (14 domains)

Domain ID domain_id2qadA00
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_id2qadB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadE00
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_id2qadF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadG01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2qadH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)