5W4L | pdb_00005w4l

Crystal structure of the non-neutralizing and ADCC-potent C11-like antibody N12-i3 in complex with HIV-1 clade A/E gp120, the CD4 mimetic M48U1, and the antibody N5-i5.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth A]	SCOP2 Family	gp120 core	8096275	4002534	SCOP2 (2022-06-29)
G [auth A]	SCOP2 Superfamily	gp120 core	8096276	3001390	SCOP2 (2022-06-29)
A [auth G]	SCOP2B Superfamily	gp120 core	8096276	3001390	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth C]	Methyltransf_25	e5w4lC1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Methyltransf_25	ECOD (develop294)
F [auth E]	Saf-Nte_pilin	e5w4lE1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: Saf-Nte_pilin	ECOD (develop294)
K [auth B]	Methyltransf_25	e5w4lB1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Methyltransf_25	ECOD (develop294)
E [auth D]	Saf-Nte_pilin	e5w4lD1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: Saf-Nte_pilin	ECOD (develop294)
J [auth I]	Methyltransf_25	e5w4lI1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Methyltransf_25	ECOD (develop294)
D [auth L]	Saf-Nte_pilin	e5w4lL1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: Saf-Nte_pilin	ECOD (develop294)
I [auth F]	Methyltransf_25	e5w4lF1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Methyltransf_25	ECOD (develop294)
C [auth H]	Saf-Nte_pilin	e5w4lH1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: Saf-Nte_pilin	ECOD (develop294)
H [auth M]	Methyltransf_25	e5w4lM1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Methyltransf_25	ECOD (develop294)
B [auth N]	Saf-Nte_pilin	e5w4lN1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: Saf-Nte_pilin	ECOD (develop294)
G [auth A]	Methyltransf_25	e5w4lA1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Methyltransf_25	ECOD (develop294)
A [auth G]	Saf-Nte_pilin	e5w4lG1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: Saf-Nte_pilin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K [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)
J [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	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
F [auth E], L [auth C]	Fab N12-i3	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ401, IGKJ402, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
E [auth D], K [auth B]	Fab N12-i3	VH-CH1	Homo sapiens (human)	IGHV1-6901, IGHV1-6902, IGHV1-6908, IGHV1-6911, IGHV1-6912, IGHV1-6913, IGHV1-69D01, IGHJ301, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
D [auth L], J [auth I]	Fab N5-i5	L-LAMBDA	Homo sapiens (human)	IGLV2-2302, IGLJ201, IGLJ302, IGLJ101, IGLJ301, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
C [auth H], I [auth F]	Fab N5-i5	VH-CH1	Homo sapiens (human)	IGHV3-2304, IGHJ401, IGHJ402, IGHJ403, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
F [auth E], L [auth C]	Light Chain	IGKV3	Kappa	clade a/e 93th057 hiv-1 gp120 core	SAbDab (2026-03-20)
E [auth D], K [auth B]	Heavy Chain	IGHV1	-	clade a/e 93th057 hiv-1 gp120 core	SAbDab (2026-03-20)
D [auth L], J [auth I]	Light Chain	IGLV2	Lambda	clade a/e 93th057 hiv-1 gp120 core	SAbDab (2026-03-20)
C [auth H], I [auth F]	Heavy Chain	IGHV3	-	clade a/e 93th057 hiv-1 gp120 core	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth E], L [auth C]	Antibody N12-i3 light chain	-	-	-
E [auth D], K [auth B]	Antibody N12-i3 Fab heavy chain	-	-	-
D [auth L], J [auth I]	Antibody N5-i5 light chain	-	-	-
C [auth H], I [auth F]	Antibody N5-i5 Fab heavy chain	-	-	-
B [auth N], H [auth M]	CD4 mimetic peptide M48U1	-	-	-
A [auth G], G [auth A]	clade A/E 93TH057 HIV-1 gp120 core	-	viral process membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virion component viral membrane viral envelope virion membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G], G [auth A]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A [auth G], G [auth A]	IPR036377	Gp120 core superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth N], H [auth M]	DPR
B [auth N], H [auth M]	MPT
B [auth N], H [auth M]	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109
B [auth N], H [auth M]	U2X	Parent Component: TYR RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100

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.