5B4W

Crystal structure of Plexin inhibitor complex

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PF01403	e5b4wD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF01403	ECOD (1.6)
A	PF01403	e5b4wA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF01403	ECOD (1.6)
B	PF01403	e5b4wB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF01403	ECOD (1.6)
C	PF01403	e5b4wC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF01403	ECOD (1.6)
E	PF01403	e5b4wE1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF01403	ECOD (1.6)
E	PF01437	e5b4wE2	A: few secondary structure elements	X: Trefoil/Plexin domain-like (From Topology)	H: Trefoil/Plexin domain-like (From Topology)	T: Trefoil/Plexin domain-like	F: PF01437	ECOD (1.6)
F	PF01403	e5b4wF1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF01403	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
C	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
E	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
E	3.30.1680.10	Alpha Beta	2-Layer Sandwich	ligand-binding face of the semaphorins, domain 2	ligand-binding face of the semaphorins, domain 2	CATH (4.3.0)
F	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	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	PF01437	Plexin repeat (PSI)	Plexin repeat	-	Family
A, B, C, D, E A, B, C, D, E, F	PF01403	Sema domain (Sema)	Sema domain	-	Repeat

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	Plexin-B1	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity GTPase activating protein binding protein binding binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity GTPase activating protein binding protein binding binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity semaphorin receptor binding signaling receptor binding	positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity biological regulation positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity multicellular organismal process positive regulation of nervous system development axonogenesis regulation of cellular process cell projection organization positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity biological regulation positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity multicellular organismal process positive regulation of nervous system development axonogenesis regulation of cellular process cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process regulation of biological process regulation of cell projection organization positive regulation of cell development nervous system development generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell morphogenesis cellular component organization regulation of nervous system development neurogenesis positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process cellular component organization or biogenesis positive regulation of axonogenesis regulation of anatomical structure morphogenesis positive regulation of cellular process regulation of multicellular organismal development plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development cellular process regulation of plasma membrane bounded cell projection organization cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction Rho protein signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of cytoskeleton organization regulation of organelle organization organelle organization cytoskeleton organization cell migration cell motility regulation of cell motility regulation of locomotion regulation of cell migration locomotion regulation of cell shape regulation of cell morphogenesis regulation of biological quality negative regulation of cell population proliferation cell population proliferation negative regulation of biological process osteoblast proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of osteoblast proliferation regulation of osteoblast proliferation cell surface receptor signaling pathway semaphorin-plexin signaling pathway bone maturation animal organ development developmental maturation skeletal system development ossification anatomical structure maturation ossification involved in bone maturation animal organ maturation bone development inhibitory synapse assembly cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization synapse assembly cell adhesion regulation of cell adhesion negative regulation of cell adhesion semaphorin-plexin signaling pathway involved in neuron projection guidance semaphorin-plexin signaling pathway involved in axon guidance axon guidance neuron projection guidance	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex semaphorin receptor complex receptor complex extracellular region
G, H, I, J, K G, H, I, J, K, L	Synthesized cyclic peptide	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR002909	IPT domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR041362	Plexin, TIG domain 2	Domain
A, B, C, D, E A, B, C, D, E, F	IPR016201	PSI domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR008936	Rho GTPase activation protein	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR002165	Plexin repeat	Repeat
A, B, C, D, E A, B, C, D, E, F	IPR041019	Plexin, TIG domain 1	Domain
A, B, C, D, E A, B, C, D, E, F	IPR031148	Plexin family	Family
A, B, C, D, E A, B, C, D, E, F	IPR046800	Plexin, cytoplasmic RhoGTPase-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR013548	Plexin, cytoplasmic RasGAP domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036352	Sema domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001627	Sema domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: O43157	Neurodevelopmental Disorders astrocytic tumor osteosarcoma subependymal giant cell astrocytoma Down syndrome ovarian cancer malignant ependymoma oligodendroglioma prostate cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G, H, I, J, K G, H, I, J, K, L	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	DTR	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 , AA0198 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 , D-tryptophan MOD:00205
G, H, I, J, K G, H, I, J, K, L	NH2	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 , AA0198 , 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 , D-tryptophan MOD:00205 , 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 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.