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- PDB-36hb: Crystal Structure of De Novo Protein Inhibitor of eEF2K -

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Basic information

Entry
Database: PDB / ID: 36hb
TitleCrystal Structure of De Novo Protein Inhibitor of eEF2K
Components
  • CAM1
  • Peptide
  • UNK-ASN-GLU-GLU-GLU-ILE
  • UNK-MET-LEU-VAL-ILE-ILE-LYS-LEU
KeywordsDE NOVO PROTEIN / DE NOVO / EEF2K / DESIGNED PROTEIN / KINASE INHIBITOR
Function / homologySUCCINIC ACID
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.492 Å
AuthorsKlupt, K.A. / Belrose, E.G. / Jia, Z.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04427 Canada
CitationJournal: To Be Published
Title: Crystal Structure of De Novo Protein Inhibitor of eEF2K
Authors: Klupt, K.A. / Belrose, E.G. / Jia, Z.
History
DepositionJun 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: CAM1
A: CAM1
B: CAM1
D: Peptide
E: UNK-MET-LEU-VAL-ILE-ILE-LYS-LEU
G: UNK-ASN-GLU-GLU-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,64510
Polymers43,3636
Non-polymers2824
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.97, 86.97, 221.58
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-202-

NA

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Components

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Protein , 1 types, 3 molecules CAB

#1: Protein CAM1


Mass: 12823.678 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Protein/peptide , 3 types, 3 molecules DEG

#2: Protein/peptide Peptide


Mass: 3258.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide UNK-MET-LEU-VAL-ILE-ILE-LYS-LEU


Mass: 915.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide UNK-ASN-GLU-GLU-GLU-ILE


Mass: 717.722 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 26 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 60 % tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 24, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.49→44.63 Å / Num. obs: 18127 / % possible obs: 99.5 % / Redundancy: 4.1 % / CC1/2: 0.83 / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.492→44.625 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.467 / SU ML: 0.211 / Cross valid method: FREE R-VALUE / ESU R: 0.392 / ESU R Free: 0.294
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2759 882 4.866 %
Rwork0.1988 17245 -
all0.202 --
obs-18127 99.972 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.021 Å2
Baniso -1Baniso -2Baniso -3
1-0.225 Å20.112 Å20 Å2
2--0.225 Å2-0 Å2
3----0.729 Å2
Refinement stepCycle: LAST / Resolution: 2.492→44.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 18 22 3052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0123053
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163043
X-RAY DIFFRACTIONr_ext_dist_refined_b0.0040.017958
X-RAY DIFFRACTIONr_angle_refined_deg3.991.944103
X-RAY DIFFRACTIONr_angle_other_deg1.4091.7817040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1845356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.506538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.51910641
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.85910164
X-RAY DIFFRACTIONr_chiral_restr0.2110.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.023542
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02614
X-RAY DIFFRACTIONr_nbd_refined0.260.2776
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.22858
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21431
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1020.22010
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3070.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1420.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3560.295
X-RAY DIFFRACTIONr_nbd_other0.2280.2275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2620.214
X-RAY DIFFRACTIONr_mcbond_it16.5096.8661442
X-RAY DIFFRACTIONr_mcbond_other16.496.8681442
X-RAY DIFFRACTIONr_mcangle_it20.85712.2931792
X-RAY DIFFRACTIONr_mcangle_other20.85412.2951793
X-RAY DIFFRACTIONr_scbond_it22.2077.4921611
X-RAY DIFFRACTIONr_scbond_other22.2017.4931612
X-RAY DIFFRACTIONr_scangle_it29.47413.3122311
X-RAY DIFFRACTIONr_scangle_other29.46813.3122312
X-RAY DIFFRACTIONr_lrange_it30.5288.81412490
X-RAY DIFFRACTIONr_lrange_other30.52388.81212489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.492-2.5570.41740.26212320.2713060.9220.9621000.226
2.557-2.6270.343590.2411930.24512520.9240.971000.206
2.627-2.7030.29630.21611810.2212450.950.97299.91970.181
2.703-2.7850.294560.20911290.21411850.9530.9731000.172
2.785-2.8760.327550.21411130.21911680.9420.971000.182
2.876-2.9770.37520.2310790.23611310.9070.9631000.198
2.977-3.0890.357600.21110360.21910960.9120.9691000.188
3.089-3.2140.287340.21510230.21710570.9340.9711000.19
3.214-3.3560.326530.2239740.22910270.9190.9681000.206
3.356-3.5190.338480.2219170.2279650.9350.9721000.209
3.519-3.7080.237370.2018960.2039330.9670.9781000.194
3.708-3.9320.244530.1848350.1878880.9590.9831000.182
3.932-4.2010.293440.1747990.1798430.9440.9811000.177
4.201-4.5340.2410.1587420.167830.9710.9841000.167
4.534-4.9620.258410.1636940.1687350.9620.9831000.177
4.962-5.5390.266340.1936410.1976750.9610.9781000.205
5.539-6.3790.276280.2255750.2286030.9710.9671000.237
6.379-7.7730.306200.2275040.235240.950.9661000.247
7.773-10.830.138180.144150.144330.9890.9881000.18
10.83-44.6250.284120.2752670.2752790.9660.9391000.337

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