9LYS | pdb_00009lys

Crystal structure of de novo designed amantadine binding homotrimer dAIT03

PDB DOI: https://doi.org/10.2210/pdb9LYS/pdb

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

Deposited: 2025-02-20 Released: 2025-12-17
Deposition Author(s): Qihan, J., Longxing, C.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.251 (Depositor), 0.251 (DCC)
R-Value Work:
0.199 (Depositor), 0.201 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

De novo design of small molecule-regulated protein oligomers

Jin, Q., Wang, Y., Chen, D., Liao, J., Cui, Z., Fan, Y., Zeng, A., Xie, M., Cao, L.

(2026) Science

DOI: https://doi.org/10.1126/science.ady6017

Macromolecule Content

Total Structure Weight: 20.16 kDa
Atom Count: 1,472
Modeled Residue Count: 165
Deposited Residue Count: 171
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dAIT03	A, B, C	57	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
308 (Subject of Investigation/LOI) Query on 308 Download Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine C₁₀ H₁₇ N DKNWSYNQZKUICI-CHIWXEEVSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.251 (Depositor), 0.251 (DCC)
R-Value Work: 0.199 (Depositor), 0.201 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.144	α = 90
b = 81.144	β = 90
c = 56.431	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFA1303700

Revision History (Full details and data files)

Version 1.0: 2025-12-17
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.