2V5E
The structure of the GDNF:Coreceptor complex: Insights into RET signalling and heparin binding.
- PDB DOI: https://doi.org/10.2210/pdb2V5E/pdb
- Classification: RECEPTOR/GLYCOPROTEIN COMPLEX
- Organism(s): Rattus norvegicus, Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2008-10-03 Released: 2008-10-21 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.237 
- R-Value Work: 0.184 
- R-Value Observed: 0.187 
This is version 2.1 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 |
GDNF FAMILY RECEPTOR ALPHA-1 | 200 | Rattus norvegicus | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for Q62997 (Rattus norvegicus) Explore Q62997  Go to UniProtKB:  Q62997 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q62997 | ||||
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 |
GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR | 101 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P39905 (Homo sapiens) Explore P39905  Go to UniProtKB:  P39905 | |||||
PHAROS:  P39905 GTEx:  ENSG00000168621  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P39905 | ||||
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 | H [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
EDO Query on EDO | D [auth A], E [auth A], F [auth A], G [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900013 Query on PRD_900013 | C | sucrose octasulfate | Oligosaccharide / Substrate analog |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.237 
- R-Value Work: 0.184 
- R-Value Observed: 0.187 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 58.9 | α = 90 |
b = 75.7 | β = 91.9 |
c = 105.5 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XSCALE | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2008-10-21  Deposition Author(s): Parkash, V., Leppanen, V.-M., Virtanen, H., Jurvansuu, J.-M., Bespalov, M.M., Sidorova, Y.A., Runeberg-Roos, P., Saarma, M., Goldman, A.
Revision History (Full details and data files)
- Version 1.0: 2008-10-21
Type: Initial release - Version 1.1: 2014-02-05
Changes: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary - Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary