6OVF | pdb_00006ovf

Crystal Structure of the Disabled-2 (Dab2) Dab Homology Domain in Complex with Peptide STA03

• PDB DOI: https://doi.org/10.2210/pdb6OVF/pdb

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


• Deposited: 2019-05-07 Released: 2020-05-13 
• Deposition Author(s): Chavez, M., Madden, D.R.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Disabled-2 (Dab2) Dab Homology Domain in Complex with Peptide STA03

Chavez, M., Madden, D.R.

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)

Biological Assembly Evidence: gel filtration, isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 39.16 kDa 
• Atom Count: 2,923 
• Modeled Residue Count: 332 
• Deposited Residue Count: 348 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disabled homolog 2	A, B	161	Homo sapiens	Mutation(s): 0  Gene Names: DAB2, DOC2
UniProt & NIH Common Fund Data Resources
Find proteins for P98082 (Homo sapiens) Explore P98082  Go to UniProtKB:  P98082
PHAROS:  P98082 GTEx:  ENSG00000153071

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
STA03	C, D	13	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	F [auth A], G [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
MG	E [auth A], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.644	α = 90
b = 102.644	β = 90
c = 80.202	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Chavez, M., Madden, D.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01-DK104847
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20-GM113132
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	P30-DK-117469

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary