3V56

Re-refinement of PDB entry 1OSG - Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold - reveals an additonal copy of the 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
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	d3v56a_	All beta proteins	TNF-like	TNF-like	TNF-like	Soluble part of TALL-1, sTALL-1 (BAFF)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3v56b_	All beta proteins	TNF-like	TNF-like	TNF-like	Soluble part of TALL-1, sTALL-1 (BAFF)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3v56c_	All beta proteins	TNF-like	TNF-like	TNF-like	Soluble part of TALL-1, sTALL-1 (BAFF)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3v56d_	All beta proteins	TNF-like	TNF-like	TNF-like	Soluble part of TALL-1, sTALL-1 (BAFF)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3v56e_	All beta proteins	TNF-like	TNF-like	TNF-like	Soluble part of TALL-1, sTALL-1 (BAFF)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3v56f_	All beta proteins	TNF-like	TNF-like	TNF-like	Soluble part of TALL-1, sTALL-1 (BAFF)	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	TNF-like	8040716	3000061	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TNF-like	8040716	3000061	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TNF-like	8040716	3000061	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TNF-like	8040716	3000061	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	TNF-like	8040716	3000061	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TNF-like	8040716	3000061	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	TNF	e3v56A1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
B	TNF	e3v56B1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
C	TNF	e3v56C1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
D	TNF	e3v56D1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
E	TNF	e3v56E1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
F	TNF	e3v56F1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
E	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
F	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		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	PF00229	TNF(Tumour Necrosis Factor) family (TNF)	TNF(Tumour Necrosis Factor) family	-	Domain
G, H, I, J, K, G, H, I, J, K, L, M [auth Z]	PF09256	BAFF-R, TALL-1 binding (BaffR-Tall_bind)	BAFF-R, TALL-1 binding	Members of this family, which are predominantly found in the tumour necrosis factor receptor superfamily member 13c, BAFF-R, are required for binding to tumour necrosis factor ligand TALL-1 [1].	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	Tumor necrosis factor ligand superfamily member 13B	protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity cytokine activity cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding	multicellular organismal process regulation of cellular process regulation of leukocyte activation positive regulation of biological process regulation of cell activation lymphocyte activation leukocyte activation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process positive regulation of immune system process multicellular organismal process regulation of cellular process regulation of leukocyte activation positive regulation of biological process regulation of cell activation lymphocyte activation leukocyte activation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process positive regulation of immune system process positive regulation of cellular process regulation of biological process B cell costimulation B cell activation cell activation biological regulation positive regulation of B cell activation immune system process lymphocyte costimulation positive regulation of multicellular organismal process cellular process regulation of lymphocyte activation developmental process skin development animal organ development anatomical structure development B cell homeostasis multicellular organismal-level homeostasis leukocyte homeostasis homeostatic process homeostasis of number of cells lymphocyte homeostasis adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of germinal center formation response to stimulus regulation of developmental process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of germinal center formation positive regulation of response to stimulus positive regulation of developmental process regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of immune response germinal center formation positive regulation of adaptive immune response regulation of anatomical structure morphogenesis immune response regulation of adaptive immune response adaptive immune response anatomical structure morphogenesis regulation of response to stimulus anatomical structure formation involved in morphogenesis regulation of immune response cellular response to stimulus signaling signal transduction cell communication cell population proliferation B cell proliferation leukocyte proliferation mononuclear cell proliferation lymphocyte proliferation T cell activation T cell proliferation cell surface receptor signaling pathway response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus response to tumor necrosis factor positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation regulation of leukocyte cell-cell adhesion T cell costimulation positive regulation of cell population proliferation positive regulation of B cell proliferation regulation of B cell proliferation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation positive regulation of lymphocyte proliferation regulation of cell population proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation transitional one stage B cell differentiation cellular developmental process immature B cell differentiation hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation transitional stage B cell differentiation B cell differentiation cell differentiation leukocyte differentiation positive regulation of T cell proliferation regulation of T cell proliferation	anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane cell periphery plasma membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cytoplasm anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane cell periphery plasma membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cytoplasm extracellular region perinuclear region of cytoplasm extracellular space
G, H, I, J, K, G, H, I, J, K, L, M [auth Z]	BR3 derived peptive	molecular transducer activity signaling receptor activity	multicellular organismal process regulation of cellular process regulation of leukocyte activation positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation multicellular organismal process regulation of cellular process regulation of leukocyte activation positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of cellular process regulation of biological process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation biological regulation regulation of T cell activation immune system process lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process cellular process T cell costimulation regulation of lymphocyte activation regulation of B cell activation B cell costimulation B cell activation positive regulation of B cell activation positive regulation of cell population proliferation positive regulation of B cell proliferation leukocyte proliferation regulation of B cell proliferation lymphocyte proliferation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation positive regulation of lymphocyte proliferation B cell proliferation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation response to stimulus immune response adaptive immune response positive regulation of T cell proliferation T cell proliferation regulation of T cell proliferation cellular response to stimulus cell surface receptor signaling pathway signaling response to cytokine cytokine-mediated signaling pathway cell communication response to peptide cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction response to tumor necrosis factor	cell periphery plasma membrane membrane cellular anatomical entity cell surface external side of plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR051748	Tumor Necrosis Factor Ligand Superfamily	Family
A, B, C, D, E A, B, C, D, E, F	IPR006052	Tumour necrosis factor domain	Domain
G, H, I, J, K, G, H, I, J, K, L, M [auth Z]	IPR015336	Tumour necrosis factor receptor 13C, TALL-1 binding domain	Domain
G, H, I, J, K, G, H, I, J, K, L, M [auth Z]	IPR022338	Tumour necrosis factor receptor 13C	Family
G, H, I, J, K, G, H, I, J, K, L, M [auth Z]	IPR043521	Tumor necrosis factor receptor 13C/17	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: Q9Y275	multiple sclerosis ovarian cancer sarcoidosis systemic lupus erythematosus arthritic joint disease breast cancer cystic fibrosis glioblastoma interstitial cystitis large cell medulloblastoma medulloblastoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma Sjogren syndrome tuberculosis multiple sclerosis ovarian cancer sarcoidosis systemic lupus erythematosus arthritic joint disease breast cancer cystic fibrosis glioblastoma interstitial cystitis large cell medulloblastoma medulloblastoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma Sjogren syndrome tuberculosis astrocytic tumor chronic obstructive pulmonary disease Duchenne muscular dystrophy head and neck cancer invasive ductal breast carcinoma lung carcinoma Mood Disorders osteosarcoma pilocytic astrocytoma subependymal giant cell astrocytoma ulcerative colitis autoimmune disease Crohn disease gastric carcinoma hematologic disease juvenile dermatomyositis malignant glioma
G, H, I, J, K, G, H, I, J, K, L, M [auth Z]	Pharos: Q96RJ3	common variable immunodeficiency agammaglobulinemia Acquired Hypogammaglobulinemia immunodeficiency, common variable, 4 interstitial cystitis osteosarcoma tuberculosis medulloblastoma primitive neuroectodermal tumor ulcerative colitis B cell deficiency brain injury ductal breast carcinoma in situ nasopharyngeal carcinoma Sjogren syndrome

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G, H, I, J, K, G, H, I, J, K, L, M [auth Z]	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
G, H, I, J, K, G, H, I, J, K, L, M [auth Z]	NH2	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 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 , L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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.