3GBJ | pdb_00003gbj

Crystal structure of the motor domain of kinesin KIF13B bound with ADP

• PDB DOI: https://doi.org/10.2210/pdb3GBJ/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-19 Released: 2009-03-03 
• Deposition Author(s): Tong, Y., Shen, L., Shen, Y., Tempel, W., 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: 2.10 Å
• R-Value Free: 
  0.269 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the motor domain of kinesin KIF13B bound with ADP

Tong, Y., Shen, L., Shen, Y., Tempel, W., 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: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 118.68 kDa 
• Atom Count: 6,756 
• Modeled Residue Count: 894 
• Deposited Residue Count: 1,062 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KIF13B protein	A, B, C	354	Homo sapiens	Mutation(s): 0  Gene Names: KIF13B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQT8 (Homo sapiens) Explore Q9NQT8  Go to UniProtKB:  Q9NQT8
PHAROS:  Q9NQT8 GTEx:  ENSG00000197892

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], H [auth B], L [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	E [auth A], I [auth B], M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX	F [auth A], G [auth A], J [auth B], K [auth B], N [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.269 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.229	α = 90
b = 86.52	β = 106.8
c = 94.948	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Tong, Y., Shen, L., Shen, Y., Tempel, W., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description