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: 2.95 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

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: KIF13BGAKINKIAA0639
Find proteins for Q9NQT8 (Homo sapiens)
Go to UniProtKB:  Q9NQT8
NIH Common Fund Data Resources
PHAROS  Q9NQT8
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Arf-GAP with dual PH domain-containing protein 1
C, D
392Homo sapiensMutation(s): 0 
Gene Names: ADAP1CENTA1
Find proteins for O75689 (Homo sapiens)
Go to UniProtKB:  O75689
NIH Common Fund Data Resources
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IP9
Query on IP9

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
C25 H50 O22 P4
ANFYVAHJWGJYAT-QLCNXWICSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A, B, C, D
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.797α = 90
b = 115.797β = 90
c = 189.269γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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