6OGE
Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex
External Resource: Annotation
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Growth factor receptor domain-like | 8043692 | 3000398 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | L domain-like | 8043690 | 3001010 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Growth factor receptor domain-like | 8043694 | 3000398 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | L domain-like | 8043691 | 3001010 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8091527 | 3000071 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8091527 | 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) |
---|---|---|---|---|---|---|---|---|
C | V-set_8 | e6ogeC1 | 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) |
C | C1-set_1 | e6ogeC2 | 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 | C1-set_4 | e6ogeB1 | 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 | V-set | e6ogeB2 | 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) |
D | C1-set_4 | e6ogeD2 | 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) |
D | V-set | e6ogeD1 | 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 | V-set_8 | e6ogeE2 | 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) |
E | C1-set_1 | e6ogeE1 | 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) |
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 |
---|---|---|---|---|---|---|---|---|
Fab Pertuzumab | VH-CH1 | Homo sapiens (human) | IGHV3-66*01, IGHV3-66*02, IGHV3-66*04, IGHJ4*01, IGHJ4*02, IGHJ4*03, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05, IGHG1*12, IGHG1*14, IGHG1*13, IGHG1*09, IGHG1*10, IGHG1*07, IGHG1*11 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_KAPPA | IMGT (202439-0) | |
Fab Pertuzumab | L-KAPPA | Homo sapiens (human) | IGKV1-16*01, IGKV1-33*01, IGKV1D-33*01, IGKV1-39*01, IGKV1D-39*01, IGKV1D-16*01, IGKV1-NL1*01, IGKJ1*01, IGKJ2*01, IGKC*01 | V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA | IG | FAB-GAMMA-1_KAPPA | IMGT (202439-0) | |
Fab Trastuzumab | L-KAPPA | Homo sapiens (human) | IGKV1-39*01, IGKV1D-39*01, IGKJ1*01, IGKC*01 | V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA | IG | FAB-GAMMA-1_KAPPA | IMGT (202439-0) | |
Fab Trastuzumab | VH-CH1 | Homo sapiens (human) | IGHV3-66*01, IGHV3-66*02, IGHV3-66*04, IGHJ4*01, IGHJ4*02, IGHJ4*03, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05, IGHG1*12, IGHG1*14, IGHG1*13, IGHG1*09, IGHG1*10, IGHG1*07, IGHG1*11 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_KAPPA | IMGT (202439-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
Heavy Chain | IGHV3 | - | receptor tyrosine-protein kinase erbb-2 | SAbDab (2024-10-04) | |
Light Chain | IGKV1 | Kappa | receptor tyrosine-protein kinase erbb-2 | SAbDab (2024-10-04) | |
Light Chain | IGKV1 | Kappa | receptor tyrosine-protein kinase erbb-2 | SAbDab (2024-10-04) | |
Heavy Chain | IGHV3 | - | receptor tyrosine-protein kinase erbb-2 | SAbDab (2024-10-04) |
Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage
Chain | Name | Target | Provenance Source |
---|---|---|---|
Anbenitamab | ERBB2/CD340/HER2 (Domain II), ERBB2/CD340/HER2 (Domain IV), ERBB2/CD340/HER2 | Therapeutic SAbDab (2024-10-04) | |
Pertuzumab | ERBB2/CD340/HER2 | Therapeutic SAbDab (2024-10-04) | |
Runimotamab | ERBB2/CD340/HER2, CD3E, SIRPA, ERBB2/CD340/HER2 (Domain II), ERBB2/CD340/HER2 (Domain IV) | Therapeutic SAbDab (2024-10-04) | |
Trastuzumab | ERBB2/CD340/HER2, CD3E, SIRPA | Therapeutic SAbDab (2024-10-04) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00757 | Furin-like cysteine rich region (Furin-like) | Furin-like cysteine rich region | - | Domain | |
PF01030 | Receptor L domain (Recep_L_domain) | Receptor L domain | - | Repeat | |
PF14843 | Growth factor receptor domain IV (GF_recep_IV) | Growth factor receptor domain IV | This is the fourth extracellular domain of receptor tyrosine protein kinases. Interaction between this domain and the furin-like domain (Pfam:PF00757) regulates the binding of ligands to the receptor L domains (Pfam:PF01030) [1]. | Domain | |
PF07686 | Immunoglobulin V-set domain (V-set) | Immunoglobulin V-set domain | This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others. | Domain | |
PF07654 | Immunoglobulin C1-set domain (C1-set) | Immunoglobulin C1-set domain | - | Domain | |
PF07654 | Immunoglobulin C1-set domain (C1-set) | Immunoglobulin C1-set domain | - | Domain | |
PF07654 | Immunoglobulin C1-set domain (C1-set) | Immunoglobulin C1-set domain | - | Domain | |
PF07686 | Immunoglobulin V-set domain (V-set) | Immunoglobulin V-set domain | This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others. | Domain | |
PF07654 | Immunoglobulin C1-set domain (C1-set) | Immunoglobulin C1-set domain | - | Domain |