9LP2 | pdb_00009lp2

Crystal structure of de novo designed amantadine induced heterodimer dAID23.4

PDB DOI: https://doi.org/10.2210/pdb9LP2/pdb

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

Deposited: 2025-01-23 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: 2.70 Å
R-Value Free:
0.296 (Depositor), 0.296 (DCC)
R-Value Work:
0.270 (Depositor), 0.278 (DCC)

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: 101.4 kDa
Atom Count: 6,942
Modeled Residue Count: 857
Deposited Residue Count: 872
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dAID23.4L	A, B, D, G	153	Escherichia coli	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
dAID23.4S	C, E, F, H	65	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 I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth G] SDF format, chain P [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth G] MOL2 format, chain P [auth G] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth G] mmCIF format, chain P [auth G]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth D] I [auth A], J [auth A], K [auth B], L [auth B], M [auth D], N [auth D], O [auth G], P [auth G]	(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine C₁₀ H₁₇ N DKNWSYNQZKUICI-CHIWXEEVSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth G] Focus chain P [auth G] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth G] Focus chain P [auth G]