4ZSO
Crystal structure of a complex between B7-H6, a tumor cell ligand for natural cytotoxicity receptor NKp30, and an inhibitory antibody
- PDB DOI: https://doi.org/10.2210/pdb4ZSO/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3), unidentified baculovirus
- Mutation(s): No 
- Deposited: 2015-05-13 Released: 2016-05-18 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.257 
- R-Value Work: 0.226 
- R-Value Observed: 0.226 
wwPDB Validation   3D Report Full Report
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Antibody Light Chain | 214 | Homo sapiens | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Antibody Heavy Chain | 219 | Homo sapiens | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Natural cytotoxicity triggering receptor 3 ligand 1 | 253 | Homo sapiens | Mutation(s): 0  Gene Names: NCR3LG1, B7H6 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q68D85 (Homo sapiens) Explore Q68D85  Go to UniProtKB:  Q68D85 | |||||
PHAROS:  Q68D85 GTEx:  ENSG00000188211  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q68D85 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | G | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | K [auth B], L [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ACY Query on ACY | M [auth E], N [auth F] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.257 
- R-Value Work: 0.226 
- R-Value Observed: 0.226 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 89.634 | α = 90 |
b = 138.029 | β = 90 |
c = 171.441 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
HKL-2000 | data collection |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2016-05-18  Deposition Author(s): Xu, X., Li, Y., Mariuzza, R.A.
Revision History (Full details and data files)
- Version 1.0: 2016-05-18
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary