1YO8
Structure of the C-terminal domain of human thrombospondin-2
- PDB DOI: https://doi.org/10.2210/pdb1YO8/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes 
- Deposited: 2005-01-26 Released: 2005-09-27 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.284 
- R-Value Work: 0.218 
- R-Value Observed: 0.224 
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 |
thrombospondin-2 | 634 | Homo sapiens | Mutation(s): 5  Gene Names: THBS2, TSP2 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P35442 (Homo sapiens) Explore P35442  Go to UniProtKB:  P35442 | |||||
PHAROS:  P35442 GTEx:  ENSG00000186340  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P35442 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | D [auth A], E [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CA Query on CA | AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.284 
- R-Value Work: 0.218 
- R-Value Observed: 0.224 
- Space Group: I 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 93.437 | α = 90 |
b = 121.588 | β = 90 |
c = 155.33 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
SCALEPACK | data scaling |
SOLVE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
Entry History 
Deposition Data
- Released Date: 2005-09-27  Deposition Author(s): Carlson, C.B., Bernstein, D.A., Annis, D.S., Misenheimer, T.M., Hannah, B.A., Mosher, D.F., Keck, J.L.
Revision History (Full details and data files)
- Version 1.0: 2005-09-27
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary