3REP | pdb_00003rep

Crystal structure of the ILK/alpha-parvin core complex (MnATP)

• PDB DOI: https://doi.org/10.2210/pdb3REP/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-04-04 Released: 2011-04-27 
• Deposition Author(s): Fukuda, K., Qin, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the ILK/alpha-parvin core complex (MnATP)

Fukuda, K., Qin, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.38 kDa 
• Atom Count: 3,517 
• Modeled Residue Count: 392 
• Deposited Residue Count: 400 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin-linked kinase	A	271	Homo sapiens	Mutation(s): 2  Gene Names: ILK, ILK1, ILK2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13418 (Homo sapiens) Explore Q13418  Go to UniProtKB:  Q13418
PHAROS:  Q13418 GTEx:  ENSG00000166333

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-parvin	B	129	Homo sapiens	Mutation(s): 0  Gene Names: PARVA, MXRA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVD7 (Homo sapiens) Explore Q9NVD7  Go to UniProtKB:  Q9NVD7
PHAROS:  Q9NVD7 GTEx:  ENSG00000197702

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.022	α = 90
b = 116.28	β = 101.53
c = 47.284	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
StructureStudio	data collection
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Fukuda, K., Qin, J.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description