8VX7 | pdb_00008vx7

Computationally designed tunable C2 symmetric tandem repeat homodimer, bound to cyclic peptide

PDB DOI: https://doi.org/10.2210/pdb8VX7/pdb

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

Deposited: 2024-02-03 Released: 2025-02-05
Deposition Author(s): Kennedy, M.A., Stoddard, B.L., Said, M.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.299 (Depositor), 0.297 (DCC)
R-Value Work:
0.253 (Depositor), 0.255 (DCC)
R-Value Observed:
0.258 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8VX7

This is version 1.0 of the entry. See complete history.

Literature

Computationally designed tunable C2 symmetric tandem repeat homodimer, bound to cyclic peptide

Kennedy, M.A., Stoddard, B.L., Said, M.

To be published.

Macromolecule Content

Total Structure Weight: 37 kDa
Atom Count: 2,229
Modeled Residue Count: 329
Deposited Residue Count: 332
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CID7	A, B	162	synthetic construct	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MC1	C	8	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL Query on DAL	C	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
DPR Query on DPR	C	D-PEPTIDE LINKING	C₅ H₉ N O₂		--
MEA Query on MEA	C	L-PEPTIDE LINKING	C₁₀ H₁₃ N O₂		PHE
MLE Query on MLE	C	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.299 (Depositor), 0.297 (DCC)
R-Value Work: 0.253 (Depositor), 0.255 (DCC)
R-Value Observed: 0.258 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.434	α = 90
b = 79.802	β = 90
c = 105.939	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DGE-1762114
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM115545
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM139752
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	R01AG063845
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	U19AG065156

Revision History (Full details and data files)

Version 1.0: 2025-02-05
Type: Initial release

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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.