6X8N | pdb_00006x8n

Crystal Structure of H49A ABLE mutant

• PDB DOI: https://doi.org/10.2210/pdb6X8N/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-01 Released: 2020-08-26 
• Deposition Author(s): Polizzi, N.F.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

A defined structural unit enables de novo design of small-molecule-binding proteins.

Polizzi, N.F., DeGrado, W.F.

(2020) Science 369: 1227-1233

• PubMed: 32883865 
• DOI: https://doi.org/10.1126/science.abb8330
• Primary Citation Related Structures: 
  6W6X, 6W70, 6X8N


• PubMed Abstract: 
  

  The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure-a van der Mer (vdM)-that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug-protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA. [e-mail] [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 27.5 kDa 
• Atom Count: 2,220 
• Modeled Residue Count: 252 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed ABLE protein	A, B	126	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.75	α = 90.13
b = 46.44	β = 117.66
c = 47	γ = 106.89

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Polizzi, N.F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		--
National Science Foundation (NSF, United States)		--

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description