7NQA | pdb_00007nqa

Crystal structure of Nucleoporin-98 nanobody MS98-6 complex solved at 2.2A resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth C]	d7nqac_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Alpaca, Lama pacos (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
B [auth D]	d7nqad_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Alpaca, Lama pacos (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth B]	SCOP2B Superfamily	ZU5 domain-like	8102799	3002026	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ZU5 domain-like	8102799	3002026	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)
D [auth C]	zf-C3HC4	e7nqaC1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: zf-C3HC4	ECOD (develop294)
B [auth D]	Ribosomal_L14e	e7nqaD1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Ribosomal_L14e	ECOD (develop294)
C [auth B]	Lon_lid	e7nqaB1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Lon_lid	ECOD (develop294)
A	Lon_lid	e7nqaA1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Lon_lid	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

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

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth D], D [auth C]	Heavy Chain	IGHV1	-	nuclear pore complex protein nup96	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D], D [auth C]	Anti-Nup98 Nanobody MS98-6	-	-	-
A, C [auth B]	Nuclear pore complex protein Nup98-Nup96	peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity structural molecule activity structural constituent of nuclear pore	RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport establishment of protein localization protein transport intracellular protein localization RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport establishment of protein localization protein transport intracellular protein localization proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane protein-containing complex membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane protein-containing complex nuclear protein-containing complex nuclear pore membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR025574	Nucleoporin FG repeat	Repeat
A, C [auth B]	IPR037665	Nucleoporin peptidase S59-like	Family
A, C [auth B]	IPR036903	Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily	Homologous Superfamily
A, C [auth B]	IPR007230	Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain	Domain
A, C [auth B]	IPR021967	Nuclear pore complex protein NUP96, C-terminal domain	Domain

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.