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 

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Ligand Structure Quality Assessment 


This is version 1.4 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
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF13B
A, B
124Homo sapiensMutation(s): 0 
Gene Names: KIF13BGAKINKIAA0639
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQT8 (Homo sapiens)
Explore Q9NQT8 
Go to UniProtKB:  Q9NQT8
GTEx:  ENSG00000197892 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQT8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Arf-GAP with dual PH domain-containing protein 1
C, D
392Homo sapiensMutation(s): 0 
Gene Names: ADAP1CENTA1
UniProt & NIH Common Fund Data Resources
Find proteins for O75689 (Homo sapiens)
Explore O75689 
Go to UniProtKB:  O75689
GTEx:  ENSG00000105963 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75689
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IP9
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
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth B]
J [auth C]
K [auth C]
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
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 

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
  • Version 1.4: 2023-09-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary