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- PDB-9cce: structure of DYNA_1b7 -

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Basic information

Entry
Database: PDB / ID: 9cce
Titlestructure of DYNA_1b7
Components
  • DYNA_1b7
  • Dynorphin A(1-17)
KeywordsDE NOVO PROTEIN / de novo design / deep learning / disorder peptide / protein-peptide complex
Function / homology
Function and homology information


opioid peptide activity / Opioid Signalling / sensory perception / neuropeptide signaling pathway / neuronal dense core vesicle / axon terminus / Peptide ligand-binding receptors / hippocampal mossy fiber to CA3 synapse / G-protein activation / G alpha (i) signalling events ...opioid peptide activity / Opioid Signalling / sensory perception / neuropeptide signaling pathway / neuronal dense core vesicle / axon terminus / Peptide ligand-binding receptors / hippocampal mossy fiber to CA3 synapse / G-protein activation / G alpha (i) signalling events / chemical synaptic transmission / neuronal cell body / dendrite / extracellular region / plasma membrane
Similarity search - Function
Proenkephalin B / Opioid neuropeptide precursor / Vertebrate endogenous opioids neuropeptide / Endogenous opioids neuropeptides precursors signature.
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsBera, A.K. / Wu, K. / Kang, A. / Baker, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2025
Title: Design of intrinsically disordered region binding proteins.
Authors: Wu, K. / Jiang, H. / Hicks, D.R. / Liu, C. / Muratspahic, E. / Ramelot, T.A. / Liu, Y. / McNally, K. / Kenny, S. / Mihut, A. / Gaur, A. / Coventry, B. / Chen, W. / Bera, A.K. / Kang, A. / ...Authors: Wu, K. / Jiang, H. / Hicks, D.R. / Liu, C. / Muratspahic, E. / Ramelot, T.A. / Liu, Y. / McNally, K. / Kenny, S. / Mihut, A. / Gaur, A. / Coventry, B. / Chen, W. / Bera, A.K. / Kang, A. / Gerben, S. / Lamb, M.Y. / Murray, A. / Li, X. / Kennedy, M.A. / Yang, W. / Song, Z. / Schober, G. / Brierley, S.M. / O'Neill, J. / Gelb, M.H. / Montelione, G.T. / Derivery, E. / Baker, D.
History
DepositionJun 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DYNA_1b7
B: DYNA_1b7
C: Dynorphin A(1-17)
D: Dynorphin A(1-17)


Theoretical massNumber of molelcules
Total (without water)54,6964
Polymers54,6964
Non-polymers00
Water00
1
A: DYNA_1b7
D: Dynorphin A(1-17)


Theoretical massNumber of molelcules
Total (without water)27,3482
Polymers27,3482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-6 kcal/mol
Surface area11080 Å2
MethodPISA
2
B: DYNA_1b7
C: Dynorphin A(1-17)


Theoretical massNumber of molelcules
Total (without water)27,3482
Polymers27,3482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-10 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.433, 67.783, 68.360
Angle α, β, γ (deg.)90.000, 98.029, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein DYNA_1b7


Mass: 25195.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Dynorphin A(1-17) / Dyn-A17 / Dynorphin A


Mass: 2152.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01213
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: 1.88 Å3/Da / Density % sol: 34.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M Phosphate/citrate pH 4.2 and 40 % v/v PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 3.15→44.43 Å / Num. obs: 6972 / % possible obs: 98.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 84.85 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.102 / Net I/σ(I): 5.6
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 517 / CC1/2: 0.79 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→28.84 Å / SU ML: 0.4823 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.5715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.313 693 9.97 %
Rwork0.2571 6258 -
obs0.2626 6951 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.23 Å2
Refinement stepCycle: LAST / Resolution: 3.15→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3355 0 0 0 3355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223376
X-RAY DIFFRACTIONf_angle_d0.41594505
X-RAY DIFFRACTIONf_chiral_restr0.0331513
X-RAY DIFFRACTIONf_plane_restr0.003583
X-RAY DIFFRACTIONf_dihedral_angle_d15.75981392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.390.381380.31871247X-RAY DIFFRACTION98.02
3.39-3.730.341380.28491246X-RAY DIFFRACTION98.37
3.73-4.270.31641380.25431237X-RAY DIFFRACTION98
4.27-5.370.31741390.24191256X-RAY DIFFRACTION98.17
5.37-28.840.27861400.24291272X-RAY DIFFRACTION98.19

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