4NNP | pdb_00004nnp

Crystal Structure of Apo Manganese ABC transporter MntC from Staphylococcus aureus bound to an antagonistic fab fragment

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth Y]	d4nnpy2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth Y]	d4nnpy1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth L]	d4nnpl2	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 L]	d4nnpl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth X]	d4nnpx_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth H]	d4nnph_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4nnpb_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
A	d4nnpa_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Helical backbone metal receptor	8074578	3001679	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helical backbone metal receptor	8074578	3001679	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)
F [auth Y]	Asparaginase_C	e4nnpY1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Asparaginase_C	ECOD (develop294)
E [auth L]	Asparaginase_C	e4nnpL1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Asparaginase_C	ECOD (develop294)
D [auth X]	Asparaginase_C	e4nnpX1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Asparaginase_C	ECOD (develop294)
C [auth H]	Asparaginase_C	e4nnpH1	A: alpha bundles	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Asparaginase_C	ECOD (develop294)
B	ZnuA	e4nnpB1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: ZnuA	ECOD (develop294)
A	ZnuA	e4nnpA1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: ZnuA	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth X]	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)
B	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
A	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	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
E [auth L], F [auth Y]	antagonistic fab	L-KAPPA	Homo sapiens (human)	IGKV1D-1301, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
C [auth H], D [auth X]	antagonistic fab	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ601, IGHJ602, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth L], F [auth Y]	Light Chain	IGKV1	Kappa	lipoprotein	SAbDab (2026-03-20)
C [auth H], D [auth X]	Heavy Chain	IGHV3	-	lipoprotein	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth L], F [auth Y]	Light chain of antagonistic fab fragment	-	-	-
C [auth H], D [auth X]	Heavy chain of antagonistic fab fragment	-	-	-
A, B	Lipoprotein	cation binding ion binding binding metal ion binding small molecule binding	cell adhesion cellular process localization transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport	cellular anatomical structure cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006129	Adhesin B	Family
A, B	IPR050492	Bacterial metal-binding protein 9	Family
A, B	IPR006127	Periplasmic solute binding protein, ZnuA-like	Family
A, B	IPR006128	Adhesion lipoprotein PsaA-like	Family

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.