2QAD | pdb_00002qad

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


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Hd2qadh1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Hd2qadh2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Dd2qadd1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Dd2qadd2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Fd2qadf1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) CD4 V-set domains human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Fd2qadf2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C2 set domains CD4 C2-set domains human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Bd2qadb1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) CD4 V-set domains human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Bd2qadb2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C2 set domains CD4 C2-set domains human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
HSCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8091519 3000071 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8091519 3000071 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054493 3000071 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054739 3000071 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054493 3000071 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054739 3000071 SCOP2B (2022-06-29)
ASCOP2B Superfamilygp120 core 8035030 3001390 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
HCopper-binde2qadH1 A: a/b three-layered sandwichesX: Phage tail fiber protein trimerization domainH: beta-Prism IT: beta-Prism IF: Copper-bindECOD (v294.1)
DCopper-binde2qadD1 A: a/b three-layered sandwichesX: Phage tail fiber protein trimerization domainH: beta-Prism IT: beta-Prism IF: Copper-bindECOD (v294.1)
Ge2qadG1 A: a/b three-layered sandwichesX: HTHH: NudixT: NudixF:ECOD (v294.1)
CStap_Strp_toxine2qadC1 A: a/b three-layered sandwichesX: Profilin-likeH: sensor domainsT: sensor domainsF: Stap_Strp_toxinECOD (v294.1)
FCopper-binde2qadF1 A: a/b three-layered sandwichesX: Phage tail fiber protein trimerization domainH: beta-Prism IT: beta-Prism IF: Copper-bindECOD (v294.1)
BCopper-binde2qadB1 A: a/b three-layered sandwichesX: Phage tail fiber protein trimerization domainH: beta-Prism IT: beta-Prism IF: Copper-bindECOD (v294.1)
EAWSe2qadE1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: AWSECOD (v294.1)
AAWSe2qadA1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: AWSECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
D, H
412d Fab, anti-gp160 [HIV-1] VH-CH1 Homo sapiens (human) IGHV1-69*01, IGHV1-69*12, IGHV1-69*13, IGHV1-69D*01, IGHJ2*01, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_KAPPA IMGT (202611-0)
C, G
412d Fab, anti-gp160 [HIV-1] L-KAPPA Homo sapiens (human) IGKV1-5*03, IGKJ2*01, IGKC*04 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-1_KAPPA IMGT (202611-0)
B, F
CD4 1V-1C-LIKE Homo sapiens (human) CD4 V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE RPI 1V-1C-LIKE IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
D, H
Heavy ChainIGHV1 -envelope glycoprotein gp160SAbDab (2026-03-27)
C, G
Light ChainIGKV1 Kappaenvelope glycoprotein gp160SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
D, H
PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domainDomain
B, F
PF05790Immunoglobulin C2-set domain (C2-set)Immunoglobulin C2-set domainDomain
B, F
PF00047Immunoglobulin domain (ig)Immunoglobulin domainMembers of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prote ...Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
D, H
anti-HIV-1 antibody 412d heavy chain
C, G
anti-HIV-1 antibody 412d light chain---
B, F
T-cell surface glycoprotein CD4
A, E
Envelope glycoprotein gp160

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
D, H
PharosP01857
B, F
PharosP01730

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
D, H
TYS Parent Component: TYR

RESIDAA0172

PSI-MOD :  O4'-sulfo-L-tyrosine MOD:00181