6EKK

Crystal structure of GEF domain of DENND 1A in complex with Rab GTPase Rab35-GDP bound state.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of DENND1A-RAB35 complex with GDP bound state.

Srikannathasan, V.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DENN domain-containing protein 1A
A, B
393Homo sapiensMutation(s): 0 
Gene Names: DENND1A (FAM31A, KIAA1608)
Find proteins for Q8TEH3 (Homo sapiens)
Go to Gene View: DENND1A
Go to UniProtKB:  Q8TEH3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-35
C, D
176Homo sapiensMutation(s): 0 
Gene Names: RAB35 (RAB1C, RAY)
Find proteins for Q15286 (Homo sapiens)
Go to Gene View: RAB35
Go to UniProtKB:  Q15286
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
C, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 55.700α = 80.50
b = 67.990β = 76.80
c = 101.710γ = 67.06
Software Package:
Software NamePurpose
xia2data scaling
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release