3HP3 | pdb_00003hp3

Crystal structure of CXCL12

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	d3hp3a_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	Stromal cell-derived factor-1 (SDF-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3hp3b_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	Stromal cell-derived factor-1 (SDF-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3hp3c_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	Stromal cell-derived factor-1 (SDF-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3hp3d_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	Stromal cell-derived factor-1 (SDF-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3hp3e_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	Stromal cell-derived factor-1 (SDF-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3hp3f_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	Stromal cell-derived factor-1 (SDF-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d3hp3g_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	Stromal cell-derived factor-1 (SDF-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d3hp3h_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	Stromal cell-derived factor-1 (SDF-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d3hp3i_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	Stromal cell-derived factor-1 (SDF-1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d3hp3j_	Alpha and beta proteins (a+b)	IL8-like	Interleukin 8-like chemokines	Interleukin 8-like chemokines	Stromal cell-derived factor-1 (SDF-1)	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	Interleukin 8-like chemokines	8043051	3001955	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Interleukin 8-like chemokines	8043051	3001955	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Interleukin 8-like chemokines	8043051	3001955	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Interleukin 8-like chemokines	8043051	3001955	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Interleukin 8-like chemokines	8043051	3001955	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Interleukin 8-like chemokines	8043051	3001955	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Interleukin 8-like chemokines	8043051	3001955	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Interleukin 8-like chemokines	8043051	3001955	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Interleukin 8-like chemokines	8043051	3001955	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Interleukin 8-like chemokines	8043051	3001955	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	Trypsin	e3hp3A1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
B	Trypsin	e3hp3B1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
C	Trypsin	e3hp3C1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
D	Trypsin	e3hp3D1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
E	Trypsin	e3hp3E1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
F	Trypsin	e3hp3F1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
G	Trypsin	e3hp3G1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
H	Trypsin	e3hp3H1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
I	Trypsin	e3hp3I1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)
J	Trypsin	e3hp3J1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Trypsin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
E	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
F	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
G	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
H	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
I	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
J	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF00048	Small cytokines (intecrine/chemokine), interleukin-8 like (IL8)	Small cytokines (intecrine/chemokine), interleukin-8 like	Includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity. Structure contains two highly conserved disulfide bonds.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	CXCL12 protein	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding chemokine activity cytokine activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding chemokine activity cytokine activity CXCR chemokine receptor binding cell adhesion molecule binding protein-containing complex binding integrin binding	response to peptide response to stimulus response to chemical response to chemokine response to cytokine cellular response to cytokine stimulus cellular response to chemokine cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process integrin activation response to peptide response to stimulus response to chemical response to chemokine response to cytokine cellular response to cytokine stimulus cellular response to chemokine cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process integrin activation cellular component organization or biogenesis response to mechanical stimulus response to abiotic stimulus response to external stimulus response to ultrasound cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway chemokine (C-X-C motif) ligand 12 signaling pathway signaling biological regulation cytokine-mediated signaling pathway chemokine-mediated signaling pathway cell communication G protein-coupled receptor signaling pathway signal transduction developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development telencephalon cell migration central nervous system development forebrain cell migration anatomical structure development cell migration telencephalon development cell motility system development inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis defense response response to stress regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process regulation of cellular component size actin filament-based process regulation of biological quality actin polymerization or depolymerization regulation of actin filament organization actin cytoskeleton organization regulation of actin polymerization or depolymerization actin filament organization regulation of organelle organization organelle organization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization regulation of anatomical structure size chemotaxis taxis locomotion detection of external stimulus system process nervous system process sensory perception of temperature stimulus sensory perception of pain detection of temperature stimulus involved in sensory perception response to temperature stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of temperature stimulus detection of stimulus involved in sensory perception detection of temperature stimulus involved in sensory perception of pain cell chemotaxis cellular response to chemical stimulus positive regulation of monocyte chemotaxis positive regulation of locomotion regulation of cell motility regulation of response to external stimulus positive regulation of biological process positive regulation of chemotaxis positive regulation of cell migration regulation of monocyte chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration myeloid leukocyte migration positive regulation of mononuclear cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process positive regulation of cellular process regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte migration positive regulation of leukocyte chemotaxis regulation of chemotaxis monocyte chemotaxis leukocyte migration regulation of response to stimulus immune system process regulation of locomotion mononuclear cell migration leukocyte chemotaxis regulation of calcium ion import regulation of calcium ion transport regulation of localization positive regulation of calcium ion transport positive regulation of calcium ion import transport regulation of transport regulation of monoatomic ion transport establishment of localization calcium ion transport metal ion transport localization positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport calcium ion import monoatomic cation transport regulation of metal ion transport regulation of lymphocyte migration positive regulation of lymphocyte migration positive regulation of T cell migration lymphocyte migration regulation of T cell migration T cell migration cell adhesion response to decreased oxygen levels response to hypoxia response to oxygen levels negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of cellular response to stress regulation of signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication cellular response to stress regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway regulation of response to stress negative regulation of cellular process intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process DNA damage response regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway adult locomotory behavior behavior adult behavior locomotory behavior response to hormone response to endogenous stimulus response to peptide hormone response to oxygen-containing compound response to nitrogen compound detection of mechanical stimulus involved in sensory perception of pain detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of mechanical stimulus positive chemotaxis positive regulation of positive chemotaxis induction of positive chemotaxis regulation of positive chemotaxis immune response axon extension positive regulation of nervous system development regulation of growth axonogenesis developmental growth cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of axon extension involved in axon guidance positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of cell projection organization positive regulation of developmental growth regulation of cell projection organization positive regulation of cell development developmental growth involved in morphogenesis generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension regulation of nervous system development neurogenesis regulation of axon extension involved in axon guidance regulation of extent of cell growth positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process axon extension involved in axon guidance positive regulation of axon extension positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth axon guidance positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis positive regulation of growth neuron projection guidance neuron development regulation of plasma membrane bounded cell projection organization CXCL12-activated CXCR4 signaling pathway C-X-C chemokine receptor CXCR4 signaling pathway negative regulation of locomotion regulation of leukocyte adhesion to vascular endothelial cell leukocyte cell-cell adhesion negative regulation of cell adhesion leukocyte tethering or rolling negative regulation of leukocyte tethering or rolling cell-cell adhesion negative regulation of cellular extravasation cellular extravasation regulation of cell-cell adhesion negative regulation of cell migration regulation of cell adhesion negative regulation of leukocyte adhesion to vascular endothelial cell regulation of leukocyte tethering or rolling negative regulation of leukocyte migration negative regulation of leukocyte cell-cell adhesion negative regulation of immune system process leukocyte adhesion to vascular endothelial cell negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of cell motility regulation of cellular extravasation monoamine transport nitrogen compound transport regulation of catecholamine secretion organic hydroxy compound transport positive regulation of secretion by cell dopamine transport positive regulation of amine transport secretion by cell regulation of secretion by cell catecholamine transport positive regulation of secretion signal release secretion positive regulation of catecholamine secretion export from cell cell-cell signaling dopamine secretion positive regulation of dopamine secretion regulation of secretion catecholamine secretion amine transport regulation of amine transport regulation of dopamine secretion vasculature development regulation of vasculature development circulatory system development positive regulation of vasculature development regulation of leukocyte apoptotic process dendritic cell apoptotic process negative regulation of dendritic cell apoptotic process leukocyte apoptotic process negative regulation of leukocyte apoptotic process regulation of dendritic cell apoptotic process positive regulation of cell adhesion positive regulation of neuron differentiation regulation of neuron differentiation biological process involved in interspecies interaction between organisms response to other organism response to external biotic stimulus response to virus response to biotic stimulus neuron migration animal organ regeneration regeneration cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation circulatory system process blood circulation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle extracellular matrix external encapsulating structure

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR001811	Chemokine interleukin-8-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036048	Chemokine interleukin-8-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR039809	Chemokine beta/gamma/delta	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR033899	CXC Chemokine domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	Pharos: P48061	breast cancer breast carcinoma HIV infectious disease prostate cancer malignant mesothelioma dermatitis Neoplasm Metastasis coronary artery disease hematologic disease pancreatic intraductal papillary-mucinous carcinoma periodontitis Sjogren syndrome limb-girdle muscular dystrophy adenoma lung adenocarcinoma breast cancer breast carcinoma HIV infectious disease prostate cancer malignant mesothelioma dermatitis Neoplasm Metastasis coronary artery disease hematologic disease pancreatic intraductal papillary-mucinous carcinoma periodontitis Sjogren syndrome limb-girdle muscular dystrophy adenoma lung adenocarcinoma atopic eczema lung disease breast fibroadenoma MALT lymphoma medulloblastoma glioblastoma ovarian cancer hepatocellular carcinoma pancreatic intraductal papillary-mucinous neoplasm interstitial cystitis periodontitis, chronic, adult ischemic disease subependymal giant cell astrocytoma adrenal cortex carcinoma lung cancer atypical teratoid rhabdoid tumor lymphoplasmacytic lymphoma cancer myocardial infarction Duchenne muscular dystrophy non-small cell lung carcinoma heart disease pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia invasive ductal breast carcinoma Pick disease large cell medulloblastoma susceptibility to HIV infection Alzheimer disease lung carcinoma autoimmune disease malignant colon neoplasm breast disease malignant pancreatic neoplasm chronic periodontitis cystic fibrosis ductal breast carcinoma in situ osteosarcoma

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.