3Q13
The Structure of the Ca2+-binding, Glycosylated F-spondin Domain of F-spondin, A C2-domain Variant from Extracellular Matrix
- PDB DOI: https://doi.org/10.2210/pdb3Q13/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens
- Expression System: Drosophila
- Mutation(s): No 
- Deposited: 2010-12-16 Released: 2011-06-29 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.210 
- R-Value Work: 0.167 
- R-Value Observed: 0.169 
wwPDB Validation   3D Report Full Report
This is version 2.1 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 |
Spondin-1 | 258 | Homo sapiens | Mutation(s): 0  Gene Names: Homo sapiens, KIAA0762, SPON1, VSGP | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9HCB6 (Homo sapiens) Explore Q9HCB6  Go to UniProtKB:  Q9HCB6 | |||||
PHAROS:  Q9HCB6 GTEx:  ENSG00000262655  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9HCB6 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | D [auth A], E [auth A], F [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ACT Query on ACT | G [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M | |||
CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.210 
- R-Value Work: 0.167 
- R-Value Observed: 0.169 
- Space Group: P 6 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 120.244 | α = 90 |
b = 120.244 | β = 90 |
c = 86.362 | γ = 120 |
Software Name | Purpose |
---|---|
SBC-Collect | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2011-06-29  Deposition Author(s): Tan, K., Lawler, J.
Revision History (Full details and data files)
- Version 1.0: 2011-06-29
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary