A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.
Shahine, A., Rossjohn, J.(2020) Nat Cancer 
Experimental Data Snapshot
Starting Models: experimental
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wwPDB Validation   3D Report Full Report
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(2020) Nat Cancer 
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Antigen-presenting glycoprotein CD1d | 347 | Homo sapiens | Mutation(s): 0  Gene Names: CD1D | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P15813 (Homo sapiens) Explore P15813  Go to UniProtKB:  P15813 | |||||
PHAROS:  P15813 GTEx:  ENSG00000158473  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P15813 | ||||
Glycosylation | |||||
Glycosylation Sites: 1 | Go to GlyGen: P15813-1 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-2-microglobulin | 100 | Homo sapiens | Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769 | |||||
PHAROS:  P61769 GTEx:  ENSG00000166710  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P61769 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
T cell receptor alpha variable 10, nkt tcr alpha chain fusion | 210 | Homo sapiens | Mutation(s): 0  Gene Names: TRAV10, B2M, HDCMA22P | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for A0A0B4J240 (Homo sapiens) Explore A0A0B4J240  Go to UniProtKB:  A0A0B4J240 | |||||
PHAROS:  A0A0B4J240 GTEx:  ENSG00000211784  | |||||
Find proteins for K7N5M3 (Homo sapiens) Explore K7N5M3  Go to UniProtKB:  K7N5M3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Groups | K7N5M3A0A0B4J240 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
nkt tcr beta chain | 241 | Homo sapiens | Mutation(s): 0  Gene Names: B2M, HDCMA22P | ||
UniProt | |||||
Find proteins for K7N5M4 (Homo sapiens) Explore K7N5M4  Go to UniProtKB:  K7N5M4 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | K7N5M4 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Nanobody VHH ID12 | 119 | Lama glama | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Ligands 2 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
AGH Query on AGH | M [auth A], N [auth F] | N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE C50 H99 N O9 VQFKFAKEUMHBLV-BYSUZVQFSA-N | |||
NAG Query on NAG | O [auth F], P [auth F] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 210.667 | α = 90 |
b = 165.25 | β = 90 |
c = 84.497 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
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