5F72 | pdb_00005f72

De novo design and crystallographic validation of antibodies targeting a pre-selected epitope

• PDB DOI: https://doi.org/10.2210/pdb5F72/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2015-12-07 Released: 2016-12-14 
• Deposition Author(s): Liu, X., Taylor, R.D., Griffin, L., Coker, S., Adams, R., Ceska, T., Shi, J., Lawson, A.D.G., Baker, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Models: experimental

Literature

De novo design and crystallographic validation of antibodies targeting a pre-selected epitope

Liu, X., Coker, S., Ceska, T., Baker, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 117.93 kDa 
• Atom Count: 8,333 
• Modeled Residue Count: 1,025 
• Deposited Residue Count: 1,106 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A [auth K], B [auth C]	296	Homo sapiens	Mutation(s): 0  Gene Names: KEAP1, INRF2, KIAA0132, KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens) Explore Q14145  Go to UniProtKB:  Q14145
PHAROS:  Q14145 GTEx:  ENSG00000079999

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Single chain Fv from a Fab	C [auth T], D [auth S]	257	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.499	α = 90
b = 69.808	β = 92.23
c = 99.562	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Liu, X., Taylor, R.D., Griffin, L., Coker, S., Adams, R., Ceska, T., Shi, J., Lawson, A.D.G., Baker, T.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary