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- PDB-13iu: E. coli DnaK bound to peptide PA9 -

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Basic information

Entry
Database: PDB / ID: 13iu
TitleE. coli DnaK bound to peptide PA9
ComponentsChaperone protein DnaK
KeywordsCHAPERONE / allosteric inhibition / DnaK / molecular chaperones / peptidomimetics / proteotoxic stress
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / : / protein-folding chaperone binding / ATP binding
Similarity search - Function
Chaperone DnaK / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
: / : / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsAriza-Mateos, A. / Serganov, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112940 United States
National Science Foundation (NSF, United States)2143170 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: Reengineering Protease Inhibitors to Disrupt Hsp70 Chaperone Function.
Authors: Richards, A. / Ariza-Mateos, A. / Ghosh, A. / Kim, M. / Sandler, S. / Yardumian, I. / Yawson, G. / Baryza, J. / Serganov, A. / Lupoli, T.J.
History
DepositionMay 8, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5752
Polymers23,8211
Non-polymers7541
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.454, 94.836, 116.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-813-

HOH

21A-815-

HOH

31A-827-

HOH

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Components

#1: Protein Chaperone protein DnaK / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70


Mass: 23820.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaK, Z0014, ECs0014 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: P0A6Z0
#2: Chemical ChemComp-A1DF0 / peptide PA9 / N-{(2S)-2-cyclohexyl-2-[(pyrazine-2-carbonyl)amino]acetyl}-L-phenylalanyl-L-prolyl-L-norvalyl-L-phenylalanine


Type: peptide-like, Peptide-like / Mass: 753.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H51N7O7 / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002607
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NH4F and 2.2 M (NH4)2SO4

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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: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.87→28.5 Å / Num. obs: 16389 / % possible obs: 92.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 36.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.053 / Net I/σ(I): 8
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 860 / CC1/2: 0.434 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→26.97 Å / SU ML: 0.2692 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.9135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 738 4.65 %
Rwork0.2411 15142 -
obs0.2421 15880 89.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.45 Å2
Refinement stepCycle: LAST / Resolution: 1.87→26.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 55 64 1735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631720
X-RAY DIFFRACTIONf_angle_d1.07512329
X-RAY DIFFRACTIONf_chiral_restr0.0607276
X-RAY DIFFRACTIONf_plane_restr0.0098309
X-RAY DIFFRACTIONf_dihedral_angle_d8.1326244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-2.010.43781190.34852182X-RAY DIFFRACTION66.77
2.01-2.220.34941740.31543281X-RAY DIFFRACTION98.52
2.22-2.540.29291140.27582848X-RAY DIFFRACTION85.16
2.54-3.20.2971740.2713340X-RAY DIFFRACTION99.6
3.2-26.970.22031570.20873491X-RAY DIFFRACTION98.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.302537280147-0.2725096864220.125143415724-0.0523205714058-0.169288811198-0.01301630162830.08624342000080.2327166297210.0459262265054-0.198806100465-0.0400778313762-0.152958385662-0.332701510637-0.152040702169-2.34788035796E-70.400923400614-0.02414486186840.1159052401950.2616768495150.01189983008860.279206939945-2.34408265841-12.0236826576-47.2788568362
20.7839395976560.0611782154138-0.1365968903841.176835413310.4535109403131.193170854130.0303349188799-0.118075313312-0.121993348936-0.06244474104810.0820136176511-0.03750496852090.0387852720725-0.1421062145362.13658375135E-90.2407525637570.005566418777140.02548129144840.2743976619150.03254999061070.270263203139-5.50171169762-15.9556658029-34.8047292474
30.921790175960.1549232751370.1667438533030.6999369415710.4151828800140.07597481032810.0642173035723-0.03995636063740.118192244023-0.373098826971-0.0464998024861-0.113245759726-0.202568575396-0.178321322668-3.64093744764E-80.397706648880.0959981097012-0.03426984596190.2350110095810.03371548067110.331799709606-10.42797207220.969649007849-36.8438680494
40.3502705386270.278570023453-0.4134570983440.5011077926490.07875189585870.5567568879310.0189645584962-0.03724620347430.3375633666410.244188797224-0.1787320900670.1646324557090.1093866949980.136631303771.7875823215E-70.2698187899170.0330785448750.01138126658550.353561756299-0.04519559618470.296119345648-8.8402569507211.504427299-18.819336428
5-0.0018365960677-0.0447688901120.008961209011720.0395082116026-0.008288413913630.0446024439242-0.0371077769377-0.243200617490.643645372302-0.0410292130309-0.11933022844-0.37344148081-0.472137552901-0.162431631724-2.10556637491E-60.4952330571440.2124913725610.03493834666710.4968554630890.05875611296580.563769603677-3.55571524171-5.95705788303-28.3592821784
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 389 through 419 )A389 - 4191 - 31
22chain 'A' and (resid 420 through 508 )A420 - 50832 - 120
33chain 'A' and (resid 509 through 551 )A509 - 551121 - 163
44chain 'A' and (resid 566 through 606 )A566 - 606178 - 218
55chain 'A' and (resid 701 through 701 )B701

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