Download MendeleyA single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.
Shahine, A., Rossjohn, J.(2020) Nat Cancer
6V7Y
Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5
- DOI: 10.2210/pdb6V7Y/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, Lama glama
- Expression System: Trichoplusia ni, Escherichia coli
- Mutation(s): No
- Deposited: 2019-12-10 Released: 2020-09-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.276
- R-Value Work: 0.241
- R-Value Observed: 0.201
wwPDB Validation 3D Report Full Report
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Antigen-presenting glycoprotein CD1d | A | 347 | Homo sapiens | Mutation(s): 0 Gene Names: CD1D |  |
Find proteins for P15813 (Homo sapiens) Explore P15813 Go to UniProtKB: P15813 | |||||
NIH Common Fund Data Resources | |||||
Protein Feature ViewExpand | |||||
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Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-2-microglobulin | B | 100 | Homo sapiens | Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P |  |
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769 | |||||
NIH Common Fund Data Resources | |||||
Protein Feature ViewExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Nanobody VHH ID5 | F | 127 | Lama glama | Mutation(s): 0 |  |
Protein Feature ViewExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 2 |  | N-Glycosylation | Oligosaccharides Interaction |
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 3 |  | N-Glycosylation | Oligosaccharides Interaction |
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| AGH Query on AGH | A | N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE C50 H99 N O9 VQFKFAKEUMHBLV-BYSUZVQFSA-N |  | Ligand Interaction | |
| NAG Query on NAG | A | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | Ligand Interaction | |
| SO4 Query on SO4 | A, B | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | Ligand Interaction | |
| CL Query on CL | A, B | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.276
- R-Value Work: 0.241
- R-Value Observed: 0.201
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 73.27 | α = 90 |
| b = 73.27 | β = 90 |
| c = 261.077 | γ = 120 |
| Software Name | Purpose |
|---|---|
| BUSTER | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Deposited Date: 2019-12-10
- Released Date: 2020-09-16 Deposition Author(s): Shahine, A., Rossjohn, J.
