9XZP | pdb_00009xzp

Crystal structure of AI-designed homodimer MIYEI

PDB DOI: https://doi.org/10.2210/pdb9XZP/pdb

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

Deposited: 2025-08-27 Released: 2025-10-22
Deposition Author(s): Wei, K.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.245 (Depositor), 0.257 (DCC)
R-Value Work:
0.189 (Depositor), 0.198 (DCC)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

An Artificial Intelligence Model for Translating Natural Language into Functional de Novo Proteins

Riley, T.P., Parsa, M.S., Kalantari, P., Naderi, I., Azimian, K., Begloo, N., Matusovsky, O., Azimian, K., Wei, K.Y.

To be published.

Macromolecule Content

Total Structure Weight: 16.06 kDa
Atom Count: 1,298
Modeled Residue Count: 155
Deposited Residue Count: 156
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo protein	A, B	78	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.245 (Depositor), 0.257 (DCC)
R-Value Work: 0.189 (Depositor), 0.198 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.093	α = 90
b = 53.473	β = 112.443
c = 55.786	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
Aimless	data scaling
TRUNCATE	data processing
REFMAC	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release

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.