1N8Z
Crystal structure of extracellular domain of human HER2 complexed with Herceptin Fab
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
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
C | SCOP2 Family | L domain | 8031312 | 4003546 | SCOP2 (2022-06-29) |
C | SCOP2 Family | L domain | 8031313 | 4003546 | SCOP2 (2022-06-29) |
C | SCOP2 Family | Growth factor receptor domain | 8031314 | 4003193 | SCOP2 (2022-06-29) |
C | SCOP2 Family | Growth factor receptor domain | 8031316 | 4003193 | SCOP2 (2022-06-29) |
C | SCOP2 Superfamily | L domain-like | 8043690 | 3001010 | SCOP2 (2022-06-29) |
C | SCOP2 Superfamily | L domain-like | 8043691 | 3001010 | SCOP2 (2022-06-29) |
C | SCOP2 Superfamily | Growth factor receptor domain-like | 8043692 | 3000398 | SCOP2 (2022-06-29) |
C | SCOP2 Superfamily | Growth factor receptor domain-like | 8043694 | 3000398 | SCOP2 (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
B | V-set_8 | e1n8zB1 | 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) |
B | C1-set_1 | e1n8zB2 | 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 | C1-set_4 | e1n8zA2 | 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) |
A | V-set | e1n8zA1 | 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) |
C | Recep_L_domain | e1n8zC1 | A: beta duplicates or obligate multimers | X: Single-stranded right-handed beta-helix | H: Leucine-rich repeats (From Topology) | T: Leucine-rich repeats | F: Recep_L_domain | ECOD (1.6) |
C | GF_recep_IV | e1n8zC4 | A: few secondary structure elements | X: EGF-like | H: Growth factor receptor domain (From Topology) | T: Growth factor receptor domain | F: GF_recep_IV | ECOD (1.6) |
C | Furin-like | e1n8zC3 | A: few secondary structure elements | X: EGF-like | H: Growth factor receptor domain (From Topology) | T: Growth factor receptor domain | F: Furin-like | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
B | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
A | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
C | 3.80.20.20 | Alpha Beta | Alpha-Beta Horseshoe | 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a' | Chain A | CATH (4.3.0) |
C | 2.10.220.10 | Mainly Beta | Ribbon | Hormone Receptor, Insulin-like Growth Factor Receptor 1 | Chain A domain 2 | 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 |
---|---|---|---|---|---|---|---|---|
4D5-humanized variant 8 Fab, Herceptin Fab | VH-CH1 | Humanized (humanized) | IGHV3-66*01, IGHV3-66*02, IGHV3-66*04, IGHJ4*01, IGHJ4*02, IGHJ4*03, IGHG1*01, IGHG1*02, IGHG1*04 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_KAPPA | IMGT (202439-0) | |
4D5-humanized variant 8 Fab, Herceptin Fab | L-KAPPA | Humanized (humanized) | 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) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
Heavy Chain | IGHV3 | - | receptor protein-tyrosine kinase erbb-2 | SAbDab (2024-10-04) | |
Light Chain | IGKV1 | Kappa | receptor protein-tyrosine kinase erbb-2 | SAbDab (2024-10-04) |
Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage
Chain | Name | Target | Provenance Source |
---|---|---|---|
Trastuzumab | ERBB2/CD340/HER2, CD3E, SIRPA | Therapeutic SAbDab (2024-10-04) | |
Runimotamab | 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 |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR016245 | Tyrosine protein kinase, EGF/ERB/XmrK receptor | Family | |
IPR008266 | Tyrosine-protein kinase, active site | Active Site | |
IPR020635 | Tyrosine-protein kinase, catalytic domain | Domain | |
IPR000719 | Protein kinase domain | Domain | |
IPR036941 | Receptor L-domain superfamily | Homologous Superfamily | |
IPR032778 | Growth factor receptor domain 4 | Domain | |
IPR049328 | Epidermal growth factor receptor-like, transmembrane-juxtamembrane segment | Domain | |
IPR006212 | Furin-like repeat | Repeat | |
IPR000494 | Receptor L-domain | Domain | |
IPR017441 | Protein kinase, ATP binding site | Binding Site | |
IPR001245 | Serine-threonine/tyrosine-protein kinase, catalytic domain | Domain | |
IPR011009 | Protein kinase-like domain superfamily | Homologous Superfamily | |
IPR006211 | Furin-like cysteine-rich domain | Domain | |
IPR009030 | Growth factor receptor cysteine-rich domain superfamily | Homologous Superfamily | |
IPR050122 | Receptor Tyrosine Kinase | Family |