Crystal Structure of Pembrolizumab, a full length IgG4 antibody
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
| Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
|---|---|---|---|---|---|---|---|---|
| A | d5dk3a2 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | C1 set domains (antibody constant domain-like) | automated matches | (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
| A | d5dk3a1 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | automated matches | automated matches | (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
| C [auth F] | d5dk3f2 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | C1 set domains (antibody constant domain-like) | automated matches | (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
| C [auth F] | d5dk3f1 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | automated matches | automated matches | (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
Domain Annotation: ECOD Classification ECOD Database Homepage
| Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
|---|---|---|---|---|---|---|---|---|
| A | e5dk3A1 | A: OB-fold | X: Nucleic acid-binding protein | H: Nucleic acid-binding protein | T: HATPase_c | F: | ECOD (20:10:01) | |
| C [auth F] | e5dk3F1 | A: OB-fold | X: Nucleic acid-binding protein | H: Nucleic acid-binding protein | T: HATPase_c | F: | ECOD (20:10:01) | |
| B | e5dk3B1 | A: OB-fold | X: Nucleic acid-binding protein | H: Nucleic acid-binding protein | T: HATPase_c | F: | ECOD (20:10:01) | |
| B | e5dk3B4 | A: Lipocalins/Streptavidin | X: SAM/DNA-glycosylase | H: SAM domain-like | T: EF-hand_1, EF-hand_6, EF-hand_7 | F: | ECOD (20:10:01) | |
| D [auth G] | e5dk3G2 | A: OB-fold | X: Nucleic acid-binding protein | H: Nucleic acid-binding protein | T: HATPase_c | F: | ECOD (20:10:01) | |
| D [auth G] | e5dk3G5 | A: Lipocalins/Streptavidin | X: SAM/DNA-glycosylase | H: SAM domain-like | T: EF-hand_1, EF-hand_6, EF-hand_7 | F: | ECOD (20:10:01) |
Domain Annotation: CATH CATH Database Homepage
| Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
|---|---|---|---|---|---|---|
| A | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| C [auth F] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
| B | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (utative) |
| D [auth G] | 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, C [auth F] | INN name | L-KAPPA | Homo sapiens (human) | IGKV3D-11*01, IGKJ4*01, IGKJ4*02, IGKC*01 | V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA | IG | IG-GAMMA-4_KAPPA | IMGT (202609-0) |
| B, D [auth G] | INN name | H-GAMMA-4 | Homo sapiens (human) | IGHV1-2*02, IGHJ6*01, IGHJ6*02, IGHG4*01, IGHG4*04 | V-DOMAIN VH, C-DOMAIN CH1, C-DOMAIN CH2, C-DOMAIN CH3 | IG | IG-GAMMA-4_KAPPA | IMGT (202609-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
| Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
|---|---|---|---|---|---|
| A, C [auth F] | Light Chain | IGKV3 | Kappa | - | SAbDab (2026-03-13) |
| B, D [auth G] | Heavy Chain | IGHV1 | - | - | SAbDab (2026-03-13) |
Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage
| Chain | Name | Target | Provenance Source |
|---|---|---|---|
| A, C [auth F] | Pembrolizumab | PDCD1/CD279/PD1 | Therapeutic SAbDab (2026-03-13) |
| B, D [auth G] | Pembrolizumab | PDCD1/CD279/PD1 | Therapeutic SAbDab (2026-03-13) |
