1VBH | pdb_00001vbh

Pyruvate Phosphate Dikinase with bound Mg-PEP from Maize

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)
A	d1vbha1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	Pyruvate phosphate dikinase, C-terminal domain	Pyruvate phosphate dikinase, C-terminal domain	(Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)
A	d1vbha2	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	Phosphohistidine domain	Pyruvate phosphate dikinase, central domain	Pyruvate phosphate dikinase, central domain	(Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)
A	d1vbha3	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Pyruvate phosphate dikinase, N-terminal domain	Pyruvate phosphate dikinase, N-terminal domain	(Zea mays ) [TaxId: 4577 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8033117	3000094	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8033114	3000510	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phosphohistidine domain	8033115	3000933	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)
A	LRR_6,LRR_RI_capping	e1vbhA1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: LRR_6,LRR_RI_capping	ECOD (develop294)
A	Enolase_C	e1vbhA2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Enolase_C	ECOD (develop294)
A	Glyco_hydro_20b	e1vbhA3	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Glyco_hydro_20b	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	1.20.80.30	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein		CATH (4.3.0)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	1.10.189.10	Mainly Alpha	Orthogonal Bundle	Pyruvate Phosphate di-kinase	domain 2	CATH (4.3.0)
A	3.50.30.10	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
A	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01326	Pyruvate phosphate dikinase, AMP/ATP-binding domain (PPDK_N)	Pyruvate phosphate dikinase, AMP/ATP-binding domain	-	Family
A	PF00391	PEP-utilising enzyme, mobile domain (PEP-utilizers)	PEP-utilising enzyme, mobile domain	This domain is a "swivelling" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it.	Domain
A	PF02896	PEP-utilising enzyme, PEP-binding domain (PEP-utilizers_C)	PEP-utilising enzyme, PEP-binding domain	This entry represents a TIM barrel domain found at the C terminus of a number of PEP (phosphoenolpyruvate)-utilising proteins. In PPDK (Pyruvate phosphate dikinase) this C-terminal domain has been shown to be a PEP-binding domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	pyruvate,orthophosphate dikinase	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 kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups pyruvate, phosphate dikinase activity phosphotransferase activity, paired acceptors cation binding metal ion binding	photosynthesis metabolic process cellular process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A	IPR008279	PEP-utilising enzyme, mobile domain	Domain
A	IPR018274	PEP-utilising enzyme, active site	Active Site
A	IPR010121	Pyruvate, phosphate dikinase	Family
A	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A	IPR023151	PEP-utilising enzyme, conserved site	Conserved Site
A	IPR036637	Phosphohistidine domain superfamily	Homologous Superfamily
A	IPR002192	Pyruvate phosphate dikinase, AMP/ATP-binding	Domain
A	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily
A	IPR000121	PEP-utilising enzyme, C-terminal	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.