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.

Experimental Data Snapshot

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

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5F72

This is version 1.2 of the entry. See complete history.

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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14145
Sequence Annotations Expand
Reference Sequence

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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), 0.265 (DCC)
R-Value Work: 0.223 (Depositor), 0.223 (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

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Entry History

Deposition Data

Released Date: 2016-12-14

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.