2YNM | pdb_00002ynm

Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family 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)
B	d2ynmb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Prochlorococcus marinus ) [TaxId: 1219 ],	SCOPe (2.08)
A	d2ynma_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Prochlorococcus marinus ) [TaxId: 1219 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Simibi-like P-loop NTPases	8058191	3002018	SCOP2B (2022-06-29)
A	SCOP2 Family	NifH/FrxC-like	8058190	4003981	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Simibi-like P-loop NTPases	8058191	3002018	SCOP2 (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	PCP_red	e2ynmD1	A: alpha bundles	X: Alpha-beta plaits	H: Histone-related	T: Histone	F: PCP_red	ECOD (develop294)
D	TPP_enzyme_C	e2ynmD2	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: TPP_enzyme_C	ECOD (develop294)
C	Glyco_hydro_106	e2ynmC1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_106	ECOD (develop294)
B	LSM	e2ynmB1	A: alpha bundles	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: LSM	ECOD (develop294)
A	Flav_NS3-hel_C	e2ynmA2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Flav_NS3-hel_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
D	1.10.8.550	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF08369	Proto-chlorophyllide reductase 57 kD subunit (PCP_red)	Proto-chlorophyllide reductase 57 kD subunit	-	Family
D	PF00148	Nitrogenase component 1 type Oxidoreductase (Oxidored_nitro)	Nitrogenase component 1 type Oxidoreductase		Domain
C	PF00148	Nitrogenase component 1 type Oxidoreductase (Oxidored_nitro)	Nitrogenase component 1 type Oxidoreductase		Domain
A, B	PF00142	4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family (Fer4_NifH)	4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on iron-sulfur proteins as donors catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor oxidoreductase activity, acting on the CH-CH group of donors	carbohydrate metabolic process biosynthetic process photosynthesis carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process pigment biosynthetic process light-independent chlorophyll biosynthetic process carbohydrate metabolic process biosynthetic process photosynthesis carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process pigment biosynthetic process light-independent chlorophyll biosynthetic process tetrapyrrole biosynthetic process porphyrin-containing compound metabolic process chlorophyll biosynthetic process	-
C	LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on iron-sulfur proteins as donors catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor oxidoreductase activity, acting on the CH-CH group of donors	pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process pigment biosynthetic process light-independent chlorophyll biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process chlorophyll biosynthetic process carbohydrate metabolic process photosynthesis pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process pigment biosynthetic process light-independent chlorophyll biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process chlorophyll biosynthetic process carbohydrate metabolic process photosynthesis carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process	-
A, B	LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on iron-sulfur proteins as donors catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor oxidoreductase activity, acting on the CH-CH group of donors	pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process pigment biosynthetic process light-independent chlorophyll biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process chlorophyll biosynthetic process carbohydrate metabolic process photosynthesis pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process pigment biosynthetic process light-independent chlorophyll biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process chlorophyll biosynthetic process carbohydrate metabolic process photosynthesis carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR013580	Light-independent protochlorophyllide reductase subunit B-like, C-terminal	Domain
D	IPR016209	Protochlorophyllide reductase, ChlB, light independent	Family
D	IPR000510	Nitrogenase/oxidoreductase, component 1	Domain
D	IPR042298	Proto-chlorophyllide reductase, C-terminal	Homologous Superfamily
D	IPR005969	Light-independent protochlorophyllide reductase, B subunit	Family
D	IPR050152	ChlB/BchB/BchZ	Family
C	IPR000510	Nitrogenase/oxidoreductase, component 1	Domain
C	IPR005970	Light-independent protochlorophyllide reductase, N subunit	Family
C	IPR050293	Light-independent protochlorophyllide reductase	Family
A, B	IPR030655	NifH/chlL conserved site	Conserved Site
A, B	IPR000392	NifH/frxC family	Family
A, B	IPR005971	Light-independent protochlorophyllide reductase, iron-sulphur ATP-binding protein	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.