2DD8
Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody
External Resource: Annotation
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 [auth S] | SCOP2B Superfamily | SARS coronavirus receptor-binding domain-like | 8041894 | 3001706 | 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) |
---|---|---|---|---|---|---|---|---|
B [auth L] | C1-set | e2dd8L2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set | ECOD (1.6) |
B [auth L] | V-set_3 | e2dd8L1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_3 | ECOD (1.6) |
C [auth S] | Spike_rec_bind | e2dd8S1 | A: a+b three layers | X: Coronavirus spike protein receptor-binding domain (From Homology) | H: Coronavirus spike protein receptor-binding domain | T: Beta-coronavirus spike protein receptor-binding domain | F: Spike_rec_bind | ECOD (1.6) |
A [auth H] | V-set_8 | e2dd8H1 | 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 | e2dd8H2 | 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) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
B [auth L] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
C [auth S] | 3.30.70.1840 | Alpha Beta | 2-Layer Sandwich | Alpha-Beta Plaits | Spike protein, C-terminal core receptor binding subdomain | CATH (4.3.0) |
A [auth H] | 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 |
---|---|---|---|---|---|---|---|---|
B [auth L] | M396 Fab | L-LAMBDA | Homo sapiens (human) | IGLV3-21*03, IGLJ1*01, IGLC1*02 | V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA | IG | FAB-GAMMA-1_LAMBDA | IMGT (202442-0) |
A [auth H] | M396 Fab | VH-CH1 | Homo sapiens (human) | IGHV1-69*02, IGHV1-69*05, IGHV1-69*10, IGHJ6*01, IGHJ6*02, IGHG1*01, IGHG1*02, IGHG1*04 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_LAMBDA | IMGT (202442-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
B [auth L] | Light Chain | IGLV3 | Lambda | spike glycoprotein | SAbDab (2024-10-25) |
A [auth H] | Heavy Chain | IGHV1 | - | spike glycoprotein | SAbDab (2024-10-25) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
B [auth L] | 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 |
B [auth L] | PF07654 | Immunoglobulin C1-set domain (C1-set) | Immunoglobulin C1-set domain | - | Domain |
C [auth S] | PF09408 | Betacoronavirus spike glycoprotein S1, receptor binding (bCoV_S1_RBD) | Betacoronavirus spike glycoprotein S1, receptor binding | This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is transla ... | Domain |