3MDB

Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.952 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4

Shen, L.Tong, Y.Tempel, W.MacKenzie, F.Arrowsmith, C.H.Edwards, A.M.Bountra, C.Weigelt, J.Bochkarev, A.Park, H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kinesin-like protein KIF13B
A, B
124Homo sapiensMutation(s): 0 
Gene Names: KIF13B (GAKIN, KIAA0639)
Find proteins for Q9NQT8 (Homo sapiens)
Go to Gene View: KIF13B
Go to UniProtKB:  Q9NQT8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Arf-GAP with dual PH domain-containing protein 1
C, D
392Homo sapiensMutation(s): 0 
Gene Names: ADAP1 (CENTA1)
Find proteins for O75689 (Homo sapiens)
Go to Gene View: ADAP1
Go to UniProtKB:  O75689
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B, C, D
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
IP9
Query on IP9

Download SDF File 
Download CCD File 
C
(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane-1,2-diyl dioctanoate
L-a-Phosphatidyl-D-myo-inositol 3,4,5-triphosphate, dioctanoyl; [(2R)-3-[[(2S,3S,5R,6S)-2,6-dihydroxy-3,4,5-triphosphonooxy-cyclohexyl]oxy-hydroxy-phosphoryl]oxy-2-octanoyloxy-propyl] octanoate
C25 H50 O22 P4
ANFYVAHJWGJYAT-QLCNXWICSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.952 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 115.797α = 90.00
b = 115.797β = 90.00
c = 189.269γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-09-18
    Type: Derived calculations
  • Version 1.3: 2017-11-08
    Type: Advisory, Refinement description