5L7N

Plexin A1 extracellular fragment, domains 7-10 (IPT3-IPT6)

• PDB DOI: https://doi.org/10.2210/pdb5L7N/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-06-03 Released: 2017-03-15 
• Deposition Author(s): Kong, Y., Janssen, B.J.C., Malinauskas, T., Vangoor, V.R., Coles, C.H., Kaufmann, R., Ni, T., Gilbert, R.J.C., Padilla-Parra, S., Pasterkamp, R.J., Jones, E.Y.
• Funding Organization(s): Cancer Research UK, Medical Research Council (United Kingdom), Wellcome Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.76 kDa 
• Atom Count: 2,821 
• Modelled Residue Count: 344 
• Deposited Residue Count: 393 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plexin-A1	A	393	Mus musculus	Mutation(s): 0  Gene Names: Plxna1, Kiaa4053
UniProt
Find proteins for P70206 (Mus musculus) Explore P70206  Go to UniProtKB:  P70206

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.88	α = 90
b = 82.51	β = 90
c = 125.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Kong, Y., Janssen, B.J.C., Malinauskas, T., Vangoor, V.R., Coles, C.H., Kaufmann, R., Ni, T., Gilbert, R.J.C., Padilla-Parra, S., Pasterkamp, R.J., Jones, E.Y.

---

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	A10976
Medical Research Council (United Kingdom)	United Kingdom	G9900061
Wellcome Trust	United Kingdom	090532/Z/09/Z

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary