6FKM

Drosophila Plexin A in complex with Semaphorin 1b

• PDB DOI: https://doi.org/10.2210/pdb6FKM/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-01-24 Released: 2019-02-06 
• Deposition Author(s): Rozbesky, D., Harlos, K., Jones, E.Y.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.246 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 145.62 kDa 
• Atom Count: 8,119 
• Modelled Residue Count: 1,022 
• Deposited Residue Count: 1,293 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plexin A, isoform A	A	715	Drosophila melanogaster	Mutation(s): 0  Gene Names:  PlexA, BcDNA:GM05237, D-Plex A, Dmel\CG11081, DPlexA, lincRNA.927, plex, plex A, Plex1, plexA, PlexA1, CG11081, Dmel_CG11081
UniProt
Find proteins for Q9V491 (Drosophila melanogaster) Explore Q9V491  Go to UniProtKB:  Q9V491

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MIP07328p	B	578	Drosophila melanogaster	Mutation(s): 0  Gene Names: Sema1b, Sema-1b, Sema-1b-RB, semaphorin-like, CG6446, Dmel_CG6446
UniProt
Find proteins for Q7KK54 (Drosophila melanogaster) Explore Q7KK54  Go to UniProtKB:  Q7KK54

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], H [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: 2.96 Å
• R-Value Free: 0.246 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.94	α = 90
b = 195.09	β = 90
c = 124.84	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Rozbesky, D., Harlos, K., Jones, E.Y.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	B5R00120

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2020-06-17
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary