6F5E | pdb_00006f5e

Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_10_47 in complex JNK1a1 and JIP1 peptide

PDB DOI: https://doi.org/10.2210/pdb6F5E/pdb
Entry: 6F5E supersedes: 5LEN

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct, Homo sapiens, Mus musculus
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2017-12-01 Released: 2017-12-13
Deposition Author(s): Wu, Y., Mittl, P.R., Honegger, A., Batyuk, A., Plueckthun, A.
Funding Organization(s): Swiss National Science Foundation, European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_10_47 in complex JNK1a1 and JIP1 peptide

Wu, Y., Mittl, P.R., Honegger, A., Batyuk, A., Plueckthun, A.

To be published.

Macromolecule Content

Total Structure Weight: 79.61 kDa
Atom Count: 5,283
Modeled Residue Count: 671
Deposited Residue Count: 709
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DD_D12_10_47	A	325	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 8	B	373	Homo sapiens	Mutation(s): 0 Gene Names: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45983 (Homo sapiens) Explore P45983 Go to UniProtKB: P45983
PHAROS: P45983 GTEx: ENSG00000107643
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P45983
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C-Jun-amino-terminal kinase-interacting protein 1	C	11	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9WVI9 (Mus musculus) Explore Q9WVI9 Go to UniProtKB: Q9WVI9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WVI9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.995	α = 90
b = 76.995	β = 90
c = 330.725	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-12-13

Deposition Author(s):

This entry supersedes: 5LEN

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_166676
European Research Council		NEXTBINDERS

Revision History (Full details and data files)

Version 1.0: 2017-12-13
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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.