4PLM
Crystal Structure of Chicken Netrin-1 (LN-LE3)
- PDB DOI: https://doi.org/10.2210/pdb4PLM/pdb
- Classification: PROTEIN BINDING
- Organism(s): Gallus gallus
- Expression System: Baculoviridae
- Mutation(s): No 
- Deposited: 2014-05-18 Released: 2014-06-18 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.257 
- R-Value Work: 0.192 
- R-Value Observed: 0.199 
This is version 1.6 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 |
Netrin-1 | 432 | Gallus gallus | Mutation(s): 0  Gene Names: NTN1 | ||
UniProt | |||||
Find proteins for Q90922 (Gallus gallus) Explore Q90922  Go to UniProtKB:  Q90922 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q90922 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | B [auth A], C [auth A], D [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CA Query on CA | E [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | F [auth A], G [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
MG Query on MG | H [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.257 
- R-Value Work: 0.192 
- R-Value Observed: 0.199 
- Space Group: P 32 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 62.627 | α = 90 |
b = 62.627 | β = 90 |
c = 269.788 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
ADSC | data collection |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2014-06-18  Deposition Author(s): Xu, K., Nikolov, D.B.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM103403 |
Department of Energy (DOE, United States) | United States | DE-AC02-06CH11357 |
Revision History (Full details and data files)
- Version 1.0: 2014-06-18
Type: Initial release - Version 1.1: 2014-06-25
Changes: Database references - Version 1.2: 2015-02-25
Changes: Derived calculations - Version 1.3: 2017-09-27
Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary - Version 1.4: 2019-12-04
Changes: Author supporting evidence - Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description, Structure summary - Version 1.6: 2023-12-27
Changes: Data collection, Database references, Structure summary