2WUH

Crystal structure of the DDR2 discoidin domain bound to a triple- helical collagen peptide

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
Membrane Protein Annotation: OPM
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2wuha_	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	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	SCOP2 Family	Discoidin domain (fa58c coagulation factor 5/8 c-terminal domain)	8069042	4002473	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	galactose-binding domain-like	8069043	3000087	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)
A	F5_F8_type_C	e2wuhA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: F5_F8_type_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00754	F5/8 type C domain (F5_F8_type_C)	F5/8 type C domain	This domain is also known as the discoidin (DS) domain family [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DISCOIDIN DOMAIN RECEPTOR 2	molecular transducer activity catalytic activity, acting on a protein collagen receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity protein tyrosine kinase collagen receptor activity catalytic activity molecular transducer activity catalytic activity, acting on a protein collagen receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity protein tyrosine kinase collagen receptor activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding collagen binding protein-containing complex binding	positive regulation of response to wounding wound healing regulation of biological process response to stimulus biological regulation positive regulation of biological process regulation of response to wounding positive regulation of response to stimulus positive regulation of wound healing regulation of response to stimulus response to stress regulation of response to stress regulation of wound healing response to wounding positive regulation of response to wounding wound healing regulation of biological process response to stimulus biological regulation positive regulation of biological process regulation of response to wounding positive regulation of response to stimulus positive regulation of wound healing regulation of response to stimulus response to stress regulation of response to stress regulation of wound healing response to wounding response to decreased oxygen levels cellular response to stimulus 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 chemical response to oxygen levels response to abiotic stimulus cellular process fibroblast proliferation cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of hepatic stellate cell proliferation regulation of fibroblast proliferation positive regulation of hepatic stellate cell proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation hepatic stellate cell proliferation positive regulation of cellular process regulation of hydrogen peroxide-mediated programmed cell death programmed cell death in response to reactive oxygen species cellular response to oxidative stress negative regulation of biological process regulation of programmed cell death cellular response to chemical stress negative regulation of hydrogen peroxide-mediated programmed cell death cellular response to reactive oxygen species hydrogen peroxide-mediated programmed cell death negative regulation of cellular process negative regulation of programmed cell death response to oxygen-containing compound cell death cellular response to oxygen-containing compound response to reactive oxygen species response to oxidative stress programmed cell death positive regulation of DNA-binding transcription factor activity cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of molecular function organic cyclic compound metabolic process regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular component disassembly extracellular matrix disassembly regulation of cellular component organization extracellular matrix organization cellular component organization cellular component organization or biogenesis regulation of extracellular matrix disassembly regulation of extracellular matrix organization extracellular structure organization external encapsulating structure organization multicellular organismal process tissue remodeling regulation of multicellular organismal process regulation of tissue remodeling regulation of cell cycle phase transition cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle cell cycle regulation of cell cycle cell cycle process positive regulation of G1/S transition of mitotic cell cycle regulation of cell cycle process positive regulation of cell cycle regulation of mitotic cell cycle phase transition positive regulation of cell cycle G1/S phase transition mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle positive regulation of cell cycle phase transition G1/S transition of mitotic cell cycle mitotic cell cycle phase transition collagen fibril organization supramolecular fiber organization protein phosphorylation organonitrogen compound metabolic process protein autophosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process developmental process regulation of multicellular organismal development regulation of developmental process bone mineralization animal organ development regulation of biomineral tissue development regulation of bone mineralization tissue development multicellular organism development ossification anatomical structure development biomineral tissue development regulation of ossification chondrocyte proliferation regulation of neuron projection development positive regulation of cellular component organization cellular developmental process cell projection organization cell development neuron projection development neurogenesis neuron differentiation positive regulation of neuron projection development cell differentiation positive regulation of cell projection organization system development plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization cell activation regulation of cell activation positive regulation of hepatic stellate cell activation fibroblast activation regulation of hepatic stellate cell activation positive regulation of cell activation hepatic stellate cell activation positive regulation of multicellular organismal process cell adhesion developmental growth growth organ growth skeletal system development bone growth endochondral bone growth bone development positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process positive regulation of metabolic process regulation of phosphate metabolic process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation positive regulation of phosphorus metabolic process regulation of protein metabolic process positive regulation of kinase activity regulation of kinase activity regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of protein modification process positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of phosphorylation collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process positive regulation of collagen metabolic process positive regulation of biosynthetic process positive regulation of collagen biosynthetic process collagen metabolic process positive regulation of extracellular matrix organization positive regulation of extracellular matrix disassembly cellular response to endogenous stimulus cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to endogenous stimulus response to growth factor regulation of apoptotic process negative regulation of apoptotic process apoptotic process collagen-activated tyrosine kinase receptor signaling pathway cell surface receptor signaling pathway signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction collagen-activated signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of locomotion regulation of cell motility regulation of fibroblast migration positive regulation of fibroblast migration fibroblast migration positive regulation of cell migration regulation of locomotion ameboidal-type cell migration positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion regulation of vascular associated smooth muscle cell proliferation positive regulation of vascular associated smooth muscle cell proliferation regulation of smooth muscle cell proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction regulation of signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling regulation of vascular associated smooth muscle cell migration vascular associated smooth muscle cell migration regulation of smooth muscle cell migration positive regulation of smooth muscle cell migration smooth muscle cell migration muscle cell migration positive regulation of vascular associated smooth muscle cell migration peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation regulation of osteoblast differentiation regulation of cell differentiation osteoblast differentiation positive regulation of developmental process positive regulation of osteoblast differentiation positive regulation of cell differentiation cellular response to nitrogen compound response to organic substance response to angiotensin response to organonitrogen compound response to peptide hormone cellular response to peptide hormone stimulus cellular response to angiotensin response to nitrogen compound cellular response to organonitrogen compound response to hormone cellular response to organic substance cellular response to hormone stimulus response to mechanical stimulus response to external stimulus response to muscle stretch	intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity actin cytoskeleton non-membrane-bounded organelle protein-containing complex receptor complex anchoring junction cell junction focal adhesion cell-substrate junction intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity actin cytoskeleton non-membrane-bounded organelle protein-containing complex receptor complex anchoring junction cell junction focal adhesion cell-substrate junction cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane
B, C, D	COLLAGEN PEPTIDE	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008266	Tyrosine-protein kinase, active site	Active Site
A	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR000421	Coagulation factor 5/8 C-terminal domain	Domain
A	IPR048525	Discoidin domain-containing receptor 1/2, DS-like domain	Domain
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A	IPR002011	Tyrosine-protein kinase, receptor class II, conserved site	Conserved Site
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q16832	spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome lung adenocarcinoma lung cancer squamous cell carcinoma intellectual disability systemic mastocytosis large cell medulloblastoma lung carcinoma malignant ependymoma Adenocarcinoma of Lung malignant pancreatic neoplasm atopic eczema oligodendroglioma breast carcinoma ovarian cancer spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome lung adenocarcinoma lung cancer squamous cell carcinoma intellectual disability systemic mastocytosis large cell medulloblastoma lung carcinoma malignant ependymoma Adenocarcinoma of Lung malignant pancreatic neoplasm atopic eczema oligodendroglioma breast carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm chronic eosinophilic leukemia dermatofibrosarcoma protuberans plantar fibromatosis Emery-Dreifuss muscular dystrophy hepatocellular carcinoma squamous cell lung carcinoma interstitial lung disease tuberculosis lung large cell carcinoma malignant glioma adrenal cortex carcinoma medulloblastoma atypical teratoid rhabdoid tumor osteogenesis imperfecta pancreatic ductal adenocarcinoma breast fibroadenoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Pick disease Duchenne muscular dystrophy psoriasis gastrointestinal stromal tumor spondyloepiphyseal dysplasia idiopathic hypereosinophilic syndrome subependymal giant cell astrocytoma invasive ductal breast carcinoma ulcerative colitis malignant colon neoplasm malignant mesothelioma astrocytic tumor osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma ductal breast carcinoma in situ renal cell carcinoma glioblastoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Peptides	Beta-helical peptides	Poly-proline helix	Collagen triple helix

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, C, D	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
B, C, D	HYP	Parent Component: PRO RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 , AA0030 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359 , 4-hydroxy-L-proline MOD:00039
B, C, D	NLE	Parent Component: LEU RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 , AA0030

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.