4RQQ | pdb_00004rqq

Crystal structure of human Fab PGDM1400, a broadly reactive and potent 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)
F [auth D]	d4rqqd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d4rqqb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d4rqqh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d4rqqc2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d4rqqc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d4rqqa2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d4rqqa1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth L]	d4rqql2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth L]	d4rqql1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(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)
F [auth D]		e4rqqD1	A: thumb domain in bacteriophage RB69-like DNA polymerase I	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: Arf	F:	ECOD (20:10:01)
D [auth B]		e4rqqB1	A: thumb domain in bacteriophage RB69-like DNA polymerase I	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: Arf	F:	ECOD (20:10:01)
B [auth H]		e4rqqH1	A: thumb domain in bacteriophage RB69-like DNA polymerase I	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: Arf	F:	ECOD (20:10:01)
E [auth C]		e4rqqC1	A: thumb domain in bacteriophage RB69-like DNA polymerase I	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: Arf	F:	ECOD (20:10:01)
C [auth A]		e4rqqA1	A: thumb domain in bacteriophage RB69-like DNA polymerase I	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: Arf	F:	ECOD (20:10:01)
A [auth L]		e4rqqL1	A: thumb domain in bacteriophage RB69-like DNA polymerase I	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: Arf	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

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

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 B], F [auth D]	neutralizing	VH-CH1	Homo sapiens (human)	IGHV1-202, IGHV1-204, IGHV1-301, IGHV1-4601, IGHV1-4602, IGHV1-4603, IGHV1-6901, IGHV1-6902, IGHV1-6904, IGHV1-6905, IGHV1-6906, IGHV1-6908, IGHV1-6909, IGHV1-6910, IGHV1-6911, IGHV1-6912, IGHV1-6913, IGHV1-6914, IGHV1-69D01, IGHJ601, IGHJ602, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)
A [auth L], C [auth A], E [auth C]	neutralizing	L-KAPPA	Homo sapiens (human)	IGKV2-2801, IGKV2D-2801, IGKV2-2902, IGKV2-2903, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L], C [auth A], E [auth C]	Light Chain	IGKV2	Kappa	-	SAbDab (2026-03-13)

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth H], D [auth B], F [auth D]	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.