8GDY | pdb_00008gdy

Crystal structure of the human PDI first domain with 9 mutations

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Thioredoxin-like	8058574	3000031	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thioredoxin-like	8058574	3000031	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	Glyco_hydro_2	e8gdyA01	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Glyco_hydro_2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00085	Thioredoxin (Thioredoxin)	Thioredoxin	Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Protein disulfide-isomerase	oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor thiol oxidase activity catalytic activity isomerase activity intramolecular oxidoreductase activity catalytic activity, acting on a protein intramolecular oxidoreductase activity, transposing S-S bonds protein disulfide isomerase activity protein heterodimerization activity protein binding binding oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor thiol oxidase activity catalytic activity isomerase activity intramolecular oxidoreductase activity catalytic activity, acting on a protein intramolecular oxidoreductase activity, transposing S-S bonds protein disulfide isomerase activity protein heterodimerization activity protein binding binding protein dimerization activity RNA binding nucleic acid binding cell adhesion molecule binding protein-containing complex binding integrin binding signaling receptor binding cytoskeletal protein binding actin binding protein-disulfide reductase activity peptidyl-proline 4-dioxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen procollagen-proline dioxygenase activity peptidyl-proline dioxygenase activity 2-oxoglutarate-dependent dioxygenase activity procollagen-proline 4-dioxygenase activity dioxygenase activity enzyme binding	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide interleukin-23-mediated signaling pathway response to chemical cellular process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide interleukin-23-mediated signaling pathway response to chemical cellular process cellular response to cytokine stimulus signal transduction protein folding biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus cellular response to interleukin-12 response to interleukin-12 interleukin-12-mediated signaling pathway protein folding in endoplasmic reticulum intrinsic apoptotic signaling pathway in response to oxidative stress regulation of oxidative stress-induced intrinsic apoptotic signaling pathway regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction regulation of intracellular signal transduction intrinsic apoptotic signaling pathway regulation of signaling regulation of apoptotic process cell death apoptotic signaling pathway regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway positive regulation of substrate adhesion-dependent cell spreading regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion positive regulation of biological process cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion substrate adhesion-dependent cell spreading positive regulation of cellular process cellular localization transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization vesicle-mediated transport localization intercellular transport establishment of localization in cell Golgi vesicle transport peptide hormone processing regulation of hormone levels signaling receptor ligand precursor processing hormone metabolic process insulin processing proteolysis protein processing regulation of biological quality insulin metabolic process positive regulation of locomotion regulation of cell motility regulation of lymphocyte migration positive regulation of cell migration positive regulation of cell motility regulation of cell migration positive regulation of mononuclear cell migration cell migration regulation of immune system process cell motility regulation of mononuclear cell migration positive regulation of immune system process locomotion positive regulation of lymphocyte migration regulation of leukocyte migration positive regulation of T cell migration lymphocyte migration positive regulation of leukocyte migration leukocyte migration immune system process regulation of locomotion regulation of T cell migration mononuclear cell migration T cell migration biological process involved in interspecies interaction between organisms positive regulation of viral life cycle positive regulation of viral process viral life cycle modulation by symbiont of entry into host biological process involved in interaction with host biological process involved in symbiotic interaction regulation of viral entry into host cell regulation of viral life cycle regulation of viral process symbiont entry into host cell viral process symbiont entry into host positive regulation of viral entry into host cell positive regulation by symbiont of entry into host regulation of biological process involved in symbiotic interaction oxoacid metabolic process carboxylic acid metabolic process modified amino acid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process non-proteinogenic amino acid metabolic process macromolecule modification peptidyl-proline hydroxylation peptidyl-amino acid modification protein hydroxylation peptidyl-proline hydroxylation to 4-hydroxy-L-proline small molecule metabolic process peptidyl-proline modification protein modification process response to interleukin-7 cellular response to interleukin-7 response to endoplasmic reticulum stress	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium cell periphery cell surface membrane plasma membrane external side of plasma membrane cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle cytosol protein-containing complex catalytic complex endomembrane system endoplasmic reticulum procollagen-proline 4-dioxygenase complex oxidoreductase complex endoplasmic reticulum protein-containing complex cytoskeleton membraneless organelle intracellular membraneless organelle membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum-Golgi intermediate compartment endoplasmic reticulum chaperone complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017937	Thioredoxin, conserved site	Conserved Site
A, B	IPR005788	Protein disulfide-isomerase, thioredoxin-like domain	Domain
A, B	IPR005792	Protein disulphide isomerase	Family
A, B	IPR013766	Thioredoxin domain	Domain
A, B	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P07237	Cole-Carpenter syndrome osteogenesis imperfecta Cole-Carpenter syndrome 1 spinocerebellar ataxia type 17 osteoporosis craniosynostosis prostate cancer malignant pancreatic neoplasm myocardial ischemia oligodendroglioma astrocytic tumor osteosarcoma chronic obstructive pulmonary disease pancreatic intraductal papillary-mucinous carcinoma coronary artery disease Cole-Carpenter syndrome osteogenesis imperfecta Cole-Carpenter syndrome 1 spinocerebellar ataxia type 17 osteoporosis craniosynostosis prostate cancer malignant pancreatic neoplasm myocardial ischemia oligodendroglioma astrocytic tumor osteosarcoma chronic obstructive pulmonary disease pancreatic intraductal papillary-mucinous carcinoma coronary artery disease pilocytic astrocytoma Post-Traumatic Osteoporosis drug-induced liver injury intellectual disability lung adenocarcinoma malignant glioma medulloblastoma myopathy osteochondrodysplasia atypical teratoid rhabdoid tumor ovarian cancer pancreatic intraductal papillary-mucinous neoplasm pituitary cancer primitive neuroectodermal tumor glioblastoma psoriasis invasive ductal breast carcinoma lung cancer malignant mesothelioma mucopolysaccharidosis type 4 non-small cell lung carcinoma breast cancer pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell myeloma diabetes mellitus hydrocephalus large cell medulloblastoma malignant ependymoma

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.