4ZG1 | pdb_00004zg1

Crystal structure of a nanobody raised against KDM5B

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d4zg1f1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d4zg1f2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d4zg1e1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d4zg1e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d4zg1d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d4zg1d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d4zg1c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d4zg1c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
B	d4zg1b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
B	d4zg1b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
A	d4zg1a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
A	d4zg1a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	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	DUF4847	e4zg1F1	A: beta barrels	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.2)
E	DUF4847	e4zg1E1	A: beta barrels	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.2)
D	DUF4847	e4zg1D1	A: beta barrels	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.2)
C	DUF4847	e4zg1C1	A: beta barrels	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.2)
B	DUF4847	e4zg1B1	A: beta barrels	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.2)
A	DUF4847	e4zg1A1	A: beta barrels	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	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
A, B, C, D, E A, B, C, D, E, F	NB17	VH	Lama glama (llama)	IGHV3S301, IGHJ401	V-DOMAIN VH	IG	(VH)	IMGT (202617-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, B, C, D, E A, B, C, D, E, F	Heavy Chain	IGHV1	-	-	SAbDab (2026-05-08)

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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.