5KBD | pdb_00005kbd

Structural Studies of Transcription Factor p73 DNA Binding Domain Bound to PA26 20-mer Response Element

• PDB DOI: https://doi.org/10.2210/pdb5KBD/pdb
• NAKB: 5KBD

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


• Deposited: 2016-06-03 Released: 2016-08-31 
• Deposition Author(s): Nguyen, H.T., Huang, D.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.308 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.282 (Depositor) 

Starting Model: experimental

Literature

Structural Studies of Transcription Factor p73 DNA Binding Domain Bound to PA26 20-mer Response Element

Nguyen, H.T., Huang, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.12 kDa 
• Atom Count: 3,584 
• Modeled Residue Count: 422 
• Deposited Residue Count: 434 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor protein p73	A, B	207	Homo sapiens	Mutation(s): 0  Gene Names: TP73, P73
UniProt & NIH Common Fund Data Resources
Find proteins for O15350 (Homo sapiens) Explore O15350  Go to UniProtKB:  O15350
PHAROS:  O15350 GTEx:  ENSG00000078900

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*AP*CP*AP*AP*GP*TP*CP*T)-3')	C	10	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*AP*CP*TP*TP*GP*TP*CP*C)-3')	D	10	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.308 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.282 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.878	α = 90
b = 174.878	β = 90
c = 34.282	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Nguyen, H.T., Huang, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA009523

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description