4R2G | pdb_00004r2g

Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
B [auth F]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054493 3000071 SCOP2B (2022-06-29)
B [auth F]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054739 3000071 SCOP2B (2022-06-29)
E [auth B]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054739 3000071 SCOP2B (2022-06-29)
E [auth B]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054493 3000071 SCOP2B (2022-06-29)
K [auth L]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054493 3000071 SCOP2B (2022-06-29)
K [auth L]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054739 3000071 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054739 3000071 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054493 3000071 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Je4r2gJ1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
M [auth N]e4r2gN1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
G [auth D]e4r2gD1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
D [auth Q]e4r2gQ1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
C [auth P]e4r2gP1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
F [auth C]e4r2gC1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
L [auth M]e4r2gM1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
Ie4r2gI1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
B [auth F]e4r2gF1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
E [auth B]e4r2gB1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
K [auth L]e4r2gL1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
He4r2gH1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Stap_Strp_tox_CF:ECOD (20:10:01)
A [auth E]e4r2gE1 A: PriB N-terminal domain-likeX: Rubredoxin-relatedH: Aconitase iron-sulfur domainT: Ribonuc_2-5AF:ECOD (20:10:01)
N [auth O]e4r2gO1 A: Immunoglobulin-like beta-sandwichX: Immunoglobulin-relatedH: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeT: AWSF:ECOD (20:10:01)
P [auth K]e4r2gK1 A: Immunoglobulin-like beta-sandwichX: Immunoglobulin-relatedH: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeT: AWSF:ECOD (20:10:01)
O [auth A]e4r2gA1 A: Immunoglobulin-like beta-sandwichX: Immunoglobulin-relatedH: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeT: AWSF:ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
J2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
M [auth N]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
G [auth D]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
D [auth Q]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
C [auth P]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
F [auth C]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
L [auth M]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
I2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
B [auth F]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
E [auth B]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
K [auth L]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
H2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
A [auth E]2.170.40.20 Mainly Beta Beta Complex HIV Envelope Protein Gp120 Chain GCATH (4.3.0)
N [auth O]2.170.40.20 Mainly Beta Beta Complex HIV Envelope Protein Gp120 Chain GCATH (4.3.0)
P [auth K]2.170.40.20 Mainly Beta Beta Complex HIV Envelope Protein Gp120 Chain GCATH (4.3.0)
O [auth A]2.170.40.20 Mainly Beta Beta Complex HIV Envelope Protein Gp120 Chain GCATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
D [auth Q],
G [auth D],
J,
M [auth N]		PGT124 VH-CH1 Homo sapiens (human) IGHV4-59*01, IGHV4-59*03, IGHV4-59*08, IGHV4-4*08, IGHJ6*03, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_LAMBDA IMGT (202609-0)
C [auth P],
F [auth C],
I,
L [auth M]		PGT124 L-LAMBDA Homo sapiens (human) IGLV3-21*01, IGLJ3*02, IGLC3*03 V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA IG FAB-GAMMA-1_LAMBDA IMGT (202609-0)
B [auth F],
E [auth B],
H,
K [auth L]		CD4 1V-1C-LIKE Homo sapiens (human) CD4 V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE RPI 1V-1C-LIKE IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
D [auth Q],
G [auth D],
J,
M [auth N]		Heavy ChainIGHV4 -surface protein gp160SAbDab (2026-03-13)
C [auth P],
F [auth C],
I,
L [auth M]		Light ChainIGLV3 Lambdasurface protein gp160SAbDab (2026-03-13)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
C [auth P],
F [auth C],
I,
L [auth M]		PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domainDomain
B [auth F],
E [auth B],
H,
K [auth L]		PF05790Immunoglobulin C2-set domain (C2-set)Immunoglobulin C2-set domainDomain
B [auth F],
E [auth B],
H,
K [auth L]		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 [auth Q],
G [auth D],
J,
M [auth N]		PGT124 Heavy Chain-
C [auth P],
F [auth C],
I,
L [auth M]		PGT124 Light Chain
B [auth F],
E [auth B],
H,
K [auth L]		T-cell surface glycoprotein CD4
A [auth E],
N [auth O],
O [auth A],
P [auth K]		Surface protein gp160

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
D [auth Q],
G [auth D],
J,
M [auth N]		IPR003597Immunoglobulin C1-setDomain
D [auth Q],
G [auth D],
J,
M [auth N]		IPR013783Immunoglobulin-like foldHomologous Superfamily
D [auth Q],
G [auth D],
J,
M [auth N]		IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
D [auth Q],
G [auth D],
J,
M [auth N]		IPR013106Immunoglobulin V-set domainDomain
D [auth Q],
G [auth D],
J,
M [auth N]		IPR003599Immunoglobulin domain subtypeDomain
D [auth Q],
G [auth D],
J,
M [auth N]		IPR007110Immunoglobulin-like domainDomain
D [auth Q],
G [auth D],
J,
M [auth N]		IPR050380Immune Recognition and Response ModulatorsFamily
D [auth Q],
G [auth D],
J,
M [auth N]		IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
C [auth P],
F [auth C],
I,
L [auth M]		IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
C [auth P],
F [auth C],
I,
L [auth M]		IPR050160Major Histocompatibility Complex/ImmunoglobulinFamily
C [auth P],
F [auth C],
I,
L [auth M]		IPR003597Immunoglobulin C1-setDomain
C [auth P],
F [auth C],
I,
L [auth M]		IPR013783Immunoglobulin-like foldHomologous Superfamily
C [auth P],
F [auth C],
I,
L [auth M]		IPR007110Immunoglobulin-like domainDomain
C [auth P],
F [auth C],
I,
L [auth M]		IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
B [auth F],
E [auth B],
H,
K [auth L]		IPR021963T cell CD4 receptor C-terminal regionDomain
B [auth F],
E [auth B],
H,
K [auth L]		IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
B [auth F],
E [auth B],
H,
K [auth L]		IPR013106Immunoglobulin V-set domainDomain
B [auth F],
E [auth B],
H,
K [auth L]		IPR000973T-cell surface antigen CD4Family
B [auth F],
E [auth B],
H,
K [auth L]		IPR003599Immunoglobulin domain subtypeDomain
B [auth F],
E [auth B],
H,
K [auth L]		IPR008424Immunoglobulin C2-setDomain
B [auth F],
E [auth B],
H,
K [auth L]		IPR013151Immunoglobulin-like beta-sandwich domainDomain
B [auth F],
E [auth B],
H,
K [auth L]		IPR015274CD4, extracellularDomain
B [auth F],
E [auth B],
H,
K [auth L]		IPR013783Immunoglobulin-like foldHomologous Superfamily
B [auth F],
E [auth B],
H,
K [auth L]		IPR007110Immunoglobulin-like domainDomain
B [auth F],
E [auth B],
H,
K [auth L]		IPR003598Immunoglobulin subtype 2Domain
A [auth E],
N [auth O],
O [auth A],
P [auth K]		IPR000777Human immunodeficiency virus 1, envelope glycoprotein Gp120Domain
A [auth E],
N [auth O],
O [auth A],
P [auth K]		IPR036377Gp120 core superfamilyHomologous Superfamily
A [auth E],
N [auth O],
O [auth A],
P [auth K]		IPR000328Retroviral envelope protein GP41-likeDomain
A [auth E],
N [auth O],
O [auth A],
P [auth K]		IPR037527Envelope glycoprotein Gp160Family

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
B [auth F],
E [auth B],
H,
K [auth L]		Pharos:  P01730