4HCR

Crystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
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)
D [auth M]	d4hcrm_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth H]	d4hcrh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d4hcrl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d4hcrl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth N]	d4hcrn2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth N]	d4hcrn1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth B]	d4hcrb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth B]	d4hcrb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d4hcra2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d4hcra1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	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)
F [auth B]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055558	3000071	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054765	3000071	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054765	3000071	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055558	3000071	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)
D [auth M]	V-set_8	e4hcrM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D [auth M]	C1-set_1	e4hcrM3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
A [auth H]	V-set_8	e4hcrH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A [auth H]	C1-set_1	e4hcrH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B [auth L]	C1-set_4	e4hcrL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B [auth L]	V-set	e4hcrL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E [auth N]	C1-set_4	e4hcrN2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E [auth N]	V-set	e4hcrN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
F [auth B]	Adhes-Ig_like	e4hcrB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Adhes-Ig_like	ECOD (1.6)
F [auth B]	ICAM_N	e4hcrB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ICAM_N	ECOD (1.6)
C [auth A]	Adhes-Ig_like	e4hcrA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Adhes-Ig_like	ECOD (1.6)
C [auth A]	ICAM_N	e4hcrA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ICAM_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth N]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A [auth H], D [auth M]	PF-547659	VH-CH1	Homo sapiens (human)	IGHV1-1801, IGHJ601, IGHJ602, IGHG201, IGHG206, IGHG205, IGHG2*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2_KAPPA	IMGT (202445-0)
B [auth L], E [auth N]	PF-547659	L-KAPPA	Homo sapiens (human)	IGKV2D-2901, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2_KAPPA	IMGT (202445-0)
C [auth A], F [auth B]	MAdCAM-1 (Mucosal addressin cell adhesion molecule 1)	2C-LIKE	Homo sapiens (human)	MADCAM1*01	C-LIKE-DOMAIN C-LIKE	RPI	MADCAM1	IMGT (202445-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H], D [auth M]	Heavy Chain	IGHV1	-	mucosal addressin cell adhesion molecule 1	SAbDab (2024-11-15)
B [auth L], E [auth N]	Light Chain	IGKV2D	Kappa	mucosal addressin cell adhesion molecule 1	SAbDab (2024-11-15)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A [auth H], D [auth M]	Ontamalimab	MADCAM1	Therapeutic SAbDab (2024-11-15)
B [auth L], E [auth N]	Ontamalimab	MADCAM1	Therapeutic SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], F [auth B]	PF09085	Adhesion molecule, immunoglobulin-like (Adhes-Ig_like)	Adhesion molecule, immunoglobulin-like	Members of this family are found in a set of mucosal cellular adhesion proteins and adopt an immunoglobulin-like beta-sandwich structure, with seven strands arranged in two beta-sheets in a Greek-key topology. They are essential for recruitment of ly ...	Members of this family are found in a set of mucosal cellular adhesion proteins and adopt an immunoglobulin-like beta-sandwich structure, with seven strands arranged in two beta-sheets in a Greek-key topology. They are essential for recruitment of lymphocytes to specific tissues [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], D [auth M]	PF-547659 heavy chain	-	-	-
B [auth L], E [auth N]	PF-547659 light chain	-	-	-
C [auth A], F [auth B]	Mucosal addressin cell adhesion molecule 1	cell adhesion molecule binding protein-containing complex binding protein binding binding cell adhesion mediator activity integrin binding signaling receptor binding integrin binding involved in cell-matrix adhesion cell-matrix adhesion mediator activity	leukocyte tethering or rolling leukocyte cell-cell adhesion leukocyte migration cell adhesion cell-cell adhesion immune system process leukocyte adhesion to vascular endothelial cell cellular extravasation cell migration cellular process cell motility cell-matrix adhesion cell-substrate adhesion positive regulation of locomotion leukocyte tethering or rolling leukocyte cell-cell adhesion leukocyte migration cell adhesion cell-cell adhesion immune system process leukocyte adhesion to vascular endothelial cell cellular extravasation cell migration cellular process cell motility cell-matrix adhesion cell-substrate adhesion positive regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process regulation of leukocyte migration biological regulation positive regulation of biological process positive regulation of leukocyte migration positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration regulation of immune system process positive regulation of immune system process locomotion positive regulation of cellular process response to stimulus immune response cellular response to stimulus integrin-mediated signaling pathway cell surface receptor signaling pathway signaling cell communication signal transduction heterotypic cell-cell adhesion protein localization localization cellular localization receptor clustering cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane regulation of lymphocyte migration positive regulation of mononuclear cell migration regulation of mononuclear cell migration positive regulation of lymphocyte migration lymphocyte migration mononuclear cell migration	cellular anatomical structure membrane cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], F [auth B]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth A], F [auth B]	IPR037413	Mucosal addressin cell adhesion molecule 1	Family
C [auth A], F [auth B]	IPR015169	Adhesion molecule, immunoglobulin-like	Domain
C [auth A], F [auth B]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth A], F [auth B]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth A], F [auth B]	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A], F [auth B]	Pharos: Q13477	colitis ovarian cyst corpus luteum cyst Ovarian Cysts medulloblastoma

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.