2P69

Crystal Structure of Human Pyridoxal Phosphate Phosphatase with PLP

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2p69a1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2p69a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	HAD-like	8058828	3001890	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	HAD_2	e2p69A1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
A	UNK_F_TYPE	e2p69A2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13242	HAD-hyrolase-like (Hydrolase_like)	HAD-hyrolase-like	-	Domain
A	PF13344	Haloacid dehalogenase-like hydrolase (Hydrolase_6)	Haloacid dehalogenase-like hydrolase	This family is part of the HAD superfamily.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Pyridoxal phosphate phosphatase	phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity protein binding binding heat shock protein binding cation binding magnesium ion binding ion binding metal ion binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity protein binding binding heat shock protein binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding protein serine/threonine phosphatase activity myosin phosphatase activity identical protein binding protein homodimerization activity protein dimerization activity pyridoxal phosphatase activity	actin cytoskeleton organization actin rod assembly actin filament organization cellular component biogenesis cellular component organization organelle organization cellular component assembly actin filament bundle organization actin filament bundle assembly actin filament-based process cellular process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization actin cytoskeleton organization actin rod assembly actin filament organization cellular component biogenesis cellular component organization organelle organization cellular component assembly actin filament bundle organization actin filament bundle assembly actin filament-based process cellular process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization positive regulation of organelle organization regulation of cytoskeleton organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization regulation of actin filament-based process regulation of cellular component size positive regulation of biological process protein-containing complex disassembly positive regulation of actin filament depolymerization regulation of protein-containing complex disassembly actin filament depolymerization regulation of actin filament depolymerization regulation of biological quality positive regulation of protein-containing complex disassembly positive regulation of cellular process cellular component disassembly actin polymerization or depolymerization regulation of biological process regulation of actin filament organization protein-containing complex organization regulation of protein depolymerization positive regulation of protein depolymerization positive regulation of cytoskeleton organization biological regulation regulation of actin polymerization or depolymerization positive regulation of supramolecular fiber organization regulation of organelle organization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization protein depolymerization regulation of anatomical structure size pyridoxal phosphate catabolic process catabolic process organic hydroxy compound metabolic process organophosphate catabolic process water-soluble vitamin catabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process water-soluble vitamin metabolic process vitamin B6 catabolic process aldehyde metabolic process vitamin metabolic process vitamin catabolic process organophosphate metabolic process organic hydroxy compound catabolic process metabolic process vitamin B6 metabolic process aldehyde catabolic process small molecule catabolic process pyridoxal phosphate metabolic process pyridine-containing compound catabolic process protein dephosphorylation dephosphorylation primary metabolic process macromolecule modification protein metabolic process macromolecule metabolic process protein modification process regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell division cell cycle regulation of cell cycle cell cycle process mitotic nuclear division organelle fission regulation of mitotic nuclear division mitotic cell cycle regulation of mitotic cell cycle nuclear division mitotic cell cycle process regulation of nuclear division cellular response to nitrogen compound cellular response to stimulus cellular response to ATP response to stimulus response to organophosphorus cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound response to ATP response to purine-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical response to organic cyclic compound regulation of modification of synaptic structure regulation of synapse organization cell junction organization regulation of synapse structure or activity regulation of modification of postsynaptic structure synapse organization modification of synaptic structure modification of postsynaptic structure	cell-cell junction cellular anatomical structure anchoring junction cell junction ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell-cell junction cellular anatomical structure anchoring junction cell junction ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane intracellular anatomical structure cytoplasm cytosol synapse glutamatergic synapse lamellipodium membrane lamellipodium intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle postsynapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006357	HAD-superfamily hydrolase, subfamily IIA	Family
A	IPR006349	2-phosphoglycolate phosphatase, eukaryotic	Family
A	IPR023214	HAD superfamily	Homologous Superfamily
A	IPR036412	HAD-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q96GD0	X-linked mixed deafness with perilymphatic gusher

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.