6FKK

Drosophila Semaphorin 1b, extracellular domains 1-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 

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
MIP07328p
A
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 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 163.256α = 90.00
b = 163.256β = 90.00
c = 140.403γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
xia2data reduction
PHENIXrefinement
xia2data scaling

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