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), 0.206 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6F5E

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

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DD_D12_10_47	A	325	synthetic construct	Mutation(s): 0

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45983
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 & NIH Common Fund Data Resources
Find proteins for Q9WVI9 (Mus musculus) Explore Q9WVI9 Go to UniProtKB: Q9WVI9
IMPC: MGI:1309464
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.206 (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

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View more in-depth experimental data

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

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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.