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


Ligand Structure Quality Assessment 


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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF13BA, B124Homo sapiensMutation(s): 0 
Gene Names: KIF13BGAKINKIAA0639
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQT8 (Homo sapiens)
Explore Q9NQT8 
Go to UniProtKB:  Q9NQT8
PHAROS:  Q9NQT8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Arf-GAP with dual PH domain-containing protein 1C, D392Homo sapiensMutation(s): 0 
Gene Names: ADAP1CENTA1
UniProt & NIH Common Fund Data Resources
Find proteins for O75689 (Homo sapiens)
Explore O75689 
Go to UniProtKB:  O75689
PHAROS:  O75689
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IP9 (Subject of Investigation/LOI)
Query on IP9

Download Ideal Coordinates CCD File 
I [auth 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 Ideal Coordinates CCD File 
H [auth C], M [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth B] , J [auth C] , K [auth C] , L [auth C] , N [auth D] , O [auth D] , 
E [auth A], F [auth A], G [auth B], J [auth C], K [auth C], L [auth C], N [auth D], O [auth D], P [auth D], Q [auth D], R [auth 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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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