6FKN

Drosophila Plexin A in complex with Semaphorin 1b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.801 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.285 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of semaphorin-plexin cis interaction

Rozbesky, D.Karia, D.Alvarez, L.Harlos, K.Padilla-Parra, S.Jones, E.Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plexin A, isoform A
A, C
715Drosophila melanogasterMutation(s): 0 
Gene Names: PlexA (BcDNA:GM05237, D-Plex A, Dmel\CG11081, DPlexA, lincRNA.927, plex, plex A, Plex1, plexA, PlexA1)
Find proteins for Q9V491 (Drosophila melanogaster)
Go to UniProtKB:  Q9V491
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MIP07328p
B, D
578Drosophila melanogasterMutation(s): 0 
Gene Names: Sema1b (BcDNA:GH03186, D-semaIII, Dmel\CG6446, Sema 1b, Sema III, Sema-1b, Sema-1b-RB, sema-III, sema1b, semaphorin-like)
Find proteins for Q7KK54 (Drosophila melanogaster)
Go to UniProtKB:  Q7KK54
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
B, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.801 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.285 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 153.630α = 90.00
b = 153.630β = 90.00
c = 425.370γ = 120.00
Software Package:
Software NamePurpose
xia2data reduction
PHASERphasing
xia2data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomB5R00120

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release