4ORG | pdb_00004org

Crystal structure of human Fab CAP256-VRC26.04, a potent V1V2-directed HIV-1 neutralizing antibody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H [auth E]	d4orge_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth C]	d4orgc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d4orga_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d4orgh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth L]	d4orgl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth L]	d4orgl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d4orgb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d4orgb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth D]	d4orgd2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth D]	d4orgd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth F]	d4orgf2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth F]	d4orgf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H [auth E]	Thioredoxin	e4orgE1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (v294.1)
F [auth C]	Thioredoxin	e4orgC1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (v294.1)
D [auth A]	Thioredoxin	e4orgA1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (v294.1)
B [auth H]	Thioredoxin	e4orgH1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (v294.1)
A [auth L]		e4orgL2	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Nicotinate/Quinolinate PRTase N-terminal domain-like	F:	ECOD (v294.1)
C [auth B]	Thioredoxin	e4orgB1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (v294.1)
E [auth D]	Thioredoxin	e4orgD1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (v294.1)
G [auth F]	Thioredoxin	e4orgF1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B [auth H], D [auth A], F [auth C], H [auth E]	CAP256-VRC26.04 mAb, anti-gp120 [HIV-1], neutralizing	VH-CH1	Homo sapiens (human)	IGHV3-3018, IGHJ301, IGHJ302, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202611-0)
A [auth L], C [auth B], E [auth D], G [auth F]	CAP256-VRC26.04 mAb, anti-gp120 [HIV-1], neutralizing	L-LAMBDA	Homo sapiens (human)	IGLV1-5102, TRAJ801, IGLC102, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H], D [auth A], F [auth C], H [auth E]	Heavy Chain	IGHV3	-	-	SAbDab (2026-03-27)
A [auth L], C [auth B], E [auth D], G [auth F]	Light Chain	IGLV1	Lambda	-	SAbDab (2026-03-27)

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth H], D [auth A], F [auth C], H [auth E]	TYS	Parent Component: TYR RESID: AA0172 PSI-MOD : O4'-sulfo-L-tyrosine MOD:00181

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.