5I5K | pdb_00005i5k

Structure of complement C5 in complex with eculizumab

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Anaphylotoxins (complement system)	8037606	3000387	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	TIMP-like	8044187	3000488	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Anaphylotoxins (complement system)	8037606	3000387	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	TIMP-like	8044187	3000488	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 [auth B]	HABP4_PAI-RBP1	e5i5kB1	A: a/b three-layered sandwiches	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (v294.1)
D [auth A]	HABP4_PAI-RBP1	e5i5kA1	A: a/b three-layered sandwiches	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (v294.1)
B [auth H]	HABP4_PAI-RBP1	e5i5kH1	A: a/b three-layered sandwiches	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (v294.1)
E [auth X]	HABP4_PAI-RBP1	e5i5kX1	A: a/b three-layered sandwiches	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (v294.1)
C [auth L]	HABP4_PAI-RBP1	e5i5kL1	A: a/b three-layered sandwiches	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (v294.1)
F [auth Y]	HABP4_PAI-RBP1	e5i5kY1	A: a/b three-layered sandwiches	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: HABP4_PAI-RBP1	ECOD (v294.1)

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
B [auth H], E [auth X]	Fab eculizumab	VH-CH1	Homo sapiens (human)	IGHV1-4601, IGHV1-4602, IGHV1-4603, IGHJ401, IGHJ402, IGHJ403, IGHG103, IGHG108, IGHG1*06	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202613-0)
C [auth L], F [auth Y]	Fab eculizumab	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202613-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H], E [auth X]	Heavy Chain	IGHV1	-	complement c5	SAbDab (2026-04-10)
C [auth L], F [auth Y]	Light Chain	IGKV1	Kappa	complement c5	SAbDab (2026-04-10)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B [auth H], E [auth X]	Eculizumab	C5	Therapeutic SAbDab (2026-04-10)
C [auth L], F [auth Y]	Pexelizumab	C5	Therapeutic SAbDab (2026-04-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], D [auth A]	PF17790	Macroglobulin domain MG1 (MG1)	Macroglobulin domain MG1	This entry represents the N-terminal macroglobulin domain found in complement proteins C3, C4 and C5.	Domain
A [auth B], D [auth A]	PF01821	Anaphylotoxin-like domain (ANATO)	Anaphylotoxin-like domain	C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins. ...	C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins.	Domain
A [auth B], D [auth A]	PF17791	Macroglobulin domain MG3 (MG3)	Macroglobulin domain MG3	This entry corresponds to the MG3 domain found in complement components C3, C4 and C5.	Domain
A [auth B], D [auth A]	PF01835	MG2 domain (MG2)	MG2 domain	This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin in eukaryotes [1]. Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. How ...	This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin in eukaryotes [1]. Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. This domain is found in eukaryotic and bacterial proteins. In human A2Ms, this domain is termed macroglobulin-like (MG) domain 2 and in Salmonella enterica ser A2Ms, this is domain 4 [2] [3].	Domain
A [auth B], D [auth A]	PF00207	Alpha-2-macroglobulin family (A2M)	Alpha-2-macroglobulin family	-	Family
A [auth B], D [auth A]	PF01759	UNC-6/NTR/C345C module (NTR)	UNC-6/NTR/C345C module	Sequence similarity between netrin UNC-6 and C345C complement protein family members, and hence the existence of the UNC-6 module, was first reported in [1]. Subsequently, many additional members of the family were identified on the basis of sequence ...	Sequence similarity between netrin UNC-6 and C345C complement protein family members, and hence the existence of the UNC-6 module, was first reported in [1]. Subsequently, many additional members of the family were identified on the basis of sequence similarity between the C-terminal domains of netrins, complement proteins C3, C4, C5, secreted frizzled-related proteins, and type I pro-collagen C-proteinase enhancer proteins (PCOLCEs), which are homologous with the N-terminal domains of tissue inhibitors of metalloproteinases (TIMPs). The TIMPs are classified as a separate family in Pfam (Pfam:PF00965) [2]. This expanded domain family has been named as the NTR module [2].	Domain
A [auth B], D [auth A]	PF07678	A-macroglobulin TED domain (TED_complement)	A-macroglobulin TED domain	-	Repeat
A [auth B], D [auth A]	PF07677	A-macroglobulin receptor binding domain (A2M_recep)	A-macroglobulin receptor binding domain	This family includes the receptor binding domain region of the alpha-2-macroglobulin family.	Domain
A [auth B], D [auth A]	PF21309	Complement component 5, CUB domain (C5_CUB)	Complement component 5, CUB domain	Complement component 5 (C5) is a component of the lytic complex consisting of factors C5-C9 which attack bacterial cell membranes. This entry represents the CUB domain [1-5].	Domain
A [auth B], D [auth A]	PF07703	Alpha-2-macroglobulin bait region domain (A2M_BRD)	Alpha-2-macroglobulin bait region domain	Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and spe ...	Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. This domain is found in eukaryotic and bacterial proteins. In human A2Ms, this domain encompasses macroglobulin-like domain MG5 and 6 including bait region. In Salmonella enterica ser A2Ms, this domain encompasses MG7 and MG8 including the bait region [1] [2]. The Bait region is cleaved by proteases, followed by a large conformational change that blocks the target protease within a cage-like complex. This model of protease entrapment is recognised as the Venus flytrap mechanism [1].	Domain
A [auth B], D [auth A]	PF17789	Macroglobulin domain MG4 (MG4)	Macroglobulin domain MG4	This domain is MG4 found in complement C3 and C5 proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], D [auth A]	Complement C5	protein binding binding signaling receptor binding molecular function activator activity G protein-coupled receptor binding signaling receptor activator activity cytokine receptor binding chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity chemokine receptor binding receptor ligand activity enzyme regulator activity protein binding binding signaling receptor binding molecular function activator activity G protein-coupled receptor binding signaling receptor activator activity cytokine receptor binding chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity chemokine receptor binding receptor ligand activity enzyme regulator activity molecular function inhibitor activity peptidase regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process immune response biological regulation immunoglobulin mediated immune response adaptive immune response immune effector process regulation of response to stimulus immune system process B cell mediated immunity regulation of immune response activation of immune response cellular response to stimulus negative regulation of mononuclear cell migration negative regulation of locomotion regulation of cell motility regulation of cellular process negative regulation of biological process negative regulation of chemotaxis macrophage migration taxis negative regulation of macrophage chemotaxis cell migration regulation of mononuclear cell migration negative regulation of macrophage migration negative regulation of cell migration chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration response to external stimulus leukocyte migration negative regulation of leukocyte migration regulation of locomotion response to chemical negative regulation of response to external stimulus negative regulation of cell motility negative regulation of leukocyte chemotaxis regulation of response to external stimulus macrophage chemotaxis regulation of macrophage migration negative regulation of cellular process regulation of cell migration myeloid leukocyte migration cell motility locomotion cell chemotaxis regulation of macrophage chemotaxis negative regulation of response to stimulus regulation of chemotaxis cellular response to chemical stimulus negative regulation of immune system process mononuclear cell migration cellular process leukocyte chemotaxis multicellular organismal process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression vascular endothelial growth factor production biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of vascular endothelial growth factor production regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process regulation of chemokine production chemokine production positive regulation of chemokine production cell surface receptor signaling pathway signaling signal transduction cell communication biological process involved in interspecies interaction between organisms response to biotic stimulus response to stress innate immune response response to external biotic stimulus response to other organism defense response defense response to symbiont complement activation, GZMK pathway defense response to other organism disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing inflammatory response G protein-coupled receptor signaling pathway complement activation, alternative pathway	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex pore complex membrane attack complex other organism cell membrane other organism part
B [auth H], E [auth X]	Eculizumab heavy chain (variable domain)	-	-	-
C [auth L], F [auth Y]	Eculizumab light chain (variable domain)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], D [auth A]	IPR009048	Alpha-macroglobulin, receptor-binding	Domain
A [auth B], D [auth A]	IPR041555	Macroglobulin domain MG3	Domain
A [auth B], D [auth A]	IPR001599	Alpha-2-macroglobulin	Domain
A [auth B], D [auth A]	IPR048843	Complement component 5, CUB domain	Domain
A [auth B], D [auth A]	IPR018081	Anaphylatoxin, complement system	Homologous Superfamily
A [auth B], D [auth A]	IPR018933	Netrin module, non-TIMP type	Domain
A [auth B], D [auth A]	IPR001840	Anaphylatoxin, complement system domain	Domain
A [auth B], D [auth A]	IPR041425	Complement C3/4/5, macroglobulin domain MG1	Domain
A [auth B], D [auth A]	IPR011625	Alpha-2-macroglobulin, bait region domain	Domain
A [auth B], D [auth A]	IPR001134	Netrin domain	Domain
A [auth B], D [auth A]	IPR008993	Tissue inhibitor of metalloproteinases-like, OB-fold	Homologous Superfamily
A [auth B], D [auth A]	IPR011626	Alpha-macroglobulin-like, TED domain	Domain
A [auth B], D [auth A]	IPR000020	Anaphylatoxin/fibulin	Domain
A [auth B], D [auth A]	IPR036595	Alpha-macroglobulin, receptor-binding domain superfamily	Homologous Superfamily
A [auth B], D [auth A]	IPR002890	Macroglobulin domain	Domain
A [auth B], D [auth A]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth B], D [auth A]	IPR050473	Alpha-2-macroglobulin/Complement system	Family
A [auth B], D [auth A]	IPR008930	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Homologous Superfamily
A [auth B], D [auth A]	IPR040839	Macroglobulin domain MG4	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], D [auth A]	Pharos: P01031	complement component 5 deficiency rheumatoid arthritis peritonitis primary immunodeficiency disease pancreatic intraductal papillary-mucinous neoplasm psoriasis Secondary Peritonitis acquired paroxysmal nocturnal hemoglobinuria lung cancer malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia tuberculosis allergic rhinitis complement component 5 deficiency rheumatoid arthritis peritonitis primary immunodeficiency disease pancreatic intraductal papillary-mucinous neoplasm psoriasis Secondary Peritonitis acquired paroxysmal nocturnal hemoglobinuria lung cancer malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia tuberculosis allergic rhinitis atypical hemolytic-uremic syndrome malignant ependymoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor seborrheic infantile dermatitis atypical teratoid rhabdoid tumor glioblastoma malignant mesothelioma neuromyelitis optica ovarian cancer

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.