3MDB | pdb_00003mdb

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

• PDB DOI: https://doi.org/10.2210/pdb3MDB/pdb

• Classification: Transport Protein/Hydrolase Activator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-30 Released: 2010-08-04 
• Deposition Author(s): Shen, L., Tong, Y., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.277 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 120.29 kDa 
• Atom Count: 7,107 
• Modeled Residue Count: 911 
• Deposited Residue Count: 1,032 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF13B	A, B	124	Homo sapiens	Mutation(s): 0  Gene Names: KIF13B, GAKIN, KIAA0639
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQT8 (Homo sapiens) Explore Q9NQT8  Go to UniProtKB:  Q9NQT8
PHAROS:  Q9NQT8 GTEx:  ENSG00000197892

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Arf-GAP with dual PH domain-containing protein 1	C, D	392	Homo sapiens	Mutation(s): 0  Gene Names: ADAP1, CENTA1
UniProt & NIH Common Fund Data Resources
Find proteins for O75689 (Homo sapiens) Explore O75689  Go to UniProtKB:  O75689
PHAROS:  O75689 GTEx:  ENSG00000105963

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IP9	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	H [auth C], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	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 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.797	α = 90
b = 115.797	β = 90
c = 189.269	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-04 
Deposition Author(s): Shen, L., Tong, Y., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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