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- PDB-9lp2: Crystal structure of de novo designed amantadine induced heterodi... -

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Basic information

Entry
Database: PDB / ID: 9lp2
TitleCrystal structure of de novo designed amantadine induced heterodimer dAID23.4
Components
  • dAID23.4L
  • dAID23.4S
KeywordsDE NOVO PROTEIN / Drug induced heterodimer
Function / homology(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsQihan, J. / Longxing, C.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303700 China
CitationJournal: Science / Year: 2026
Title: De novo design of small molecule-regulated protein oligomers
Authors: Jin, Q. / Wang, Y. / Chen, D. / Liao, J. / Cui, Z. / Fan, Y. / Zeng, A. / Xie, M. / Cao, L.
History
DepositionJan 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dAID23.4L
B: dAID23.4L
C: dAID23.4S
D: dAID23.4L
E: dAID23.4S
F: dAID23.4S
G: dAID23.4L
H: dAID23.4S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,39616
Polymers100,1868
Non-polymers1,2108
Water00
1
A: dAID23.4L
C: dAID23.4S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3494
Polymers25,0472
Non-polymers3022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-9 kcal/mol
Surface area10730 Å2
MethodPISA
2
B: dAID23.4L
F: dAID23.4S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3494
Polymers25,0472
Non-polymers3022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-11 kcal/mol
Surface area10970 Å2
MethodPISA
3
D: dAID23.4L
E: dAID23.4S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3494
Polymers25,0472
Non-polymers3022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-12 kcal/mol
Surface area10800 Å2
MethodPISA
4
G: dAID23.4L
H: dAID23.4S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3494
Polymers25,0472
Non-polymers3022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-11 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.508, 72.793, 130.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
dAID23.4L


Mass: 17494.709 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein
dAID23.4S


Mass: 7551.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-308 / (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine / Amantadine


Mass: 151.249 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C10H17N / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 30% (v/v) PEG 400, 100 mM CHES/ Sodium hydroxide pH 9.5

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Data collection

DiffractionMean temperature: 181 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→29.72 Å / Num. obs: 23345 / % possible obs: 86.14 % / Redundancy: 3.7 % / CC1/2: 0.998 / Net I/σ(I): 8.09
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 1705 / CC1/2: 0.902

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.09 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2958 735 3.54 %
Rwork0.2701 --
obs-20752 86.14 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6854 0 88 0 6942
LS refinement shellResolution: 2.7→2.91 Å
RfactorNum. reflection% reflection
Rfree0.4969 138 -
Rwork0.4706 3372 -
obs--71 %

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