3WSY
SorLA Vps10p domain in complex with its own propeptide fragment
- PDB DOI: https://doi.org/10.2210/pdb3WSY/pdb
- Classification: PROTEIN BINDING
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No 
- Deposited: 2014-03-30 Released: 2015-02-04 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.11 Å
- R-Value Free: 0.232 
- R-Value Work: 0.195 
- R-Value Observed: 0.197 
This is version 1.3 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Sortilin-related receptor | 678 | Homo sapiens | Mutation(s): 0  Gene Names: SORL1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q92673 (Homo sapiens) Explore Q92673  Go to UniProtKB:  Q92673 | |||||
PHAROS:  Q92673 GTEx:  ENSG00000137642  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q92673 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
peptide from Sortilin-related receptor | B [auth C] | 15 | Homo sapiens | Mutation(s): 0  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q92673 (Homo sapiens) Explore Q92673  Go to UniProtKB:  Q92673 | |||||
PHAROS:  Q92673 GTEx:  ENSG00000137642  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q92673 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | C [auth A], D [auth A], E [auth A], F [auth A], G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.11 Å
- R-Value Free: 0.232 
- R-Value Work: 0.195 
- R-Value Observed: 0.197 
- Space Group: I 41
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 158.186 | α = 90 |
b = 158.186 | β = 90 |
c = 145.458 | γ = 90 |
Software Name | Purpose |
---|---|
UGUIS | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2015-02-04  Deposition Author(s): Kitago, Y., Nakata, Z., Nagae, M., Nogi, T., Takagi, J.
Revision History (Full details and data files)
- Version 1.0: 2015-02-04
Type: Initial release - Version 1.1: 2020-01-01
Changes: Database references, Derived calculations - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary