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- PDB-13jk: E. coli DnaK bound to peptide PA5 -

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Basic information

Entry
Database: PDB / ID: 13jk
TitleE. coli DnaK bound to peptide PA5
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
: / : / IODIDE ION / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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 9, 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

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,87618
Polymers47,6422
Non-polymers3,23516
Water52229
1
A: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0886
Polymers23,8211
Non-polymers1,2685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,78812
Polymers23,8211
Non-polymers1,96711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.805, 118.963, 36.885
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-818-

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.: 2
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-A1DHT / peptide PA5 / 1-[(2S)-2-cyclohexyl-2-{[3-cyclohexyl-N-(pyrazine-2-carbonyl)-L-alanyl]amino}acetyl]-L-prolyl-L-norvalyl-L-phenylalanine


Type: Peptide-like / Mass: 759.934 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H57N7O7 / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002609
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NH4I, 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: 2.6→30 Å / Num. obs: 13392 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 69.96 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.05 / Rrim(I) all: 0.114 / Net I/σ(I): 44.3
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 1.379 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1294 / CC1/2: 0.501 / Rpim(I) all: 0.671 / Rrim(I) all: 1.541

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→29.82 Å / SU ML: 0.4502 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.1117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2843 2387 10.03 %
Rwork0.2462 21419 -
obs0.25 13343 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.09 Å2
Refinement stepCycle: LAST / Resolution: 2.62→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 132 29 3308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563313
X-RAY DIFFRACTIONf_angle_d1.02434485
X-RAY DIFFRACTIONf_chiral_restr0.0494540
X-RAY DIFFRACTIONf_plane_restr0.0082588
X-RAY DIFFRACTIONf_dihedral_angle_d12.0625478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.670.33121290.39261135X-RAY DIFFRACTION86.63
2.67-2.730.4291380.38281209X-RAY DIFFRACTION93.22
2.73-2.790.37251420.38231254X-RAY DIFFRACTION95.03
2.79-2.860.38241380.37541270X-RAY DIFFRACTION94.94
2.86-2.940.44361290.38451234X-RAY DIFFRACTION95.05
2.94-3.020.41171390.3651269X-RAY DIFFRACTION95.78
3.02-3.120.35461390.31221297X-RAY DIFFRACTION96.77
3.12-3.230.32031440.31231229X-RAY DIFFRACTION95.68
3.23-3.360.30711450.28881296X-RAY DIFFRACTION96.58
3.36-3.510.3661350.27981231X-RAY DIFFRACTION96.13
3.52-3.70.31791460.25691298X-RAY DIFFRACTION95.69
3.7-3.930.26591330.22681240X-RAY DIFFRACTION96.08
3.93-4.230.25681430.21511281X-RAY DIFFRACTION97.33
4.23-4.660.23351400.19851286X-RAY DIFFRACTION96.94
4.66-5.330.25711420.18841295X-RAY DIFFRACTION98.63
5.33-6.70.28951490.24511289X-RAY DIFFRACTION99.58
6.7-29.820.2051560.1961306X-RAY DIFFRACTION98.78
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)
11.87178380691-0.233621613706-0.5343522229454.81916995169-1.116107307761.93113054862-0.131942083085-0.08460957377870.02187259735640.3027211096820.1341669780910.198761486328-0.386235801256-0.4165568253060.002665128665520.5320043442650.137477436033-0.08834131264740.561463454075-0.04519526741420.429993208515-15.975557112519.7684181049-15.2804222539
27.281424900081.481959622230.8123695248057.523499052351.227242121749.420735718580.4101285216410.338718560347-0.816693798463-0.203916176026-0.557402280226-2.09292452870.475806050944-0.0770272841117-0.0328632128310.954226241030.07604881799310.009873931333470.539016287463-0.09340534188881.12755991827-5.536538475323.02084122114-23.4503701212
32.321210291061.979246185741.317998491171.731997049980.5157093304313.08510190022-0.49665162437-0.3590185255960.5139506387210.09571128252560.3714637621180.333317834944-0.823717707911-0.4708220907930.1965900512830.678003226150.02588940515250.004674660410290.584244669768-0.0315041187941.042837973273.0136564520732.7499025914-19.1489879792
44.121314234190.2724357752071.28019046765.713940178762.467323286335.43075198278-0.197932247220.23231262460.846084876931-0.985073190085-0.0700405855048-0.589790135437-0.8870319534150.4936990501510.4158671432060.61554171617-0.0950069365504-0.09146636256820.6662139359040.01105042360490.7814643814419.5957073355241.7314423687-23.0908122965
51.049943297520.0642686566383-0.1840720297984.84685667831-0.2337015259871.943042366890.06859792837-0.0163790133952-0.04048017123320.241804884328-0.187397734379-0.537158201432-0.407176819550.1719135629390.077408985530.565197135184-0.08222683072190.01762137284090.514151754450.0278883303760.52094588390213.547135077221.8023762116-6.65393635633
62.02904937355-0.108841502120.5646525495062.426183537210.8754821048781.92356915011.04877883141-0.547993398791.343451762991.56594921691-0.5514967385380.783806106910.599718419704-0.74952542966-0.1976687702720.704040803466-0.0762750119420.0841469324810.842455331369-0.03797355571240.8468615423615.2427779514.195684149141.69711056525
74.59071808453-2.36274622594-0.8585551568644.12913023631-1.359113378743.12793085374-0.1658213301190.2332856155030.619540968078-0.609548832369-0.0882955218864-0.532931625432-0.2772948915780.07006782059590.1663341046330.494790565748-0.0332669017663-0.03698319818060.462114200667-0.01336435446280.542279900181-6.8100982723932.5248023718-2.60725275437
85.0029489061-0.478695822134-0.6407996323864.68119457335-1.42117358876.022123703540.04873619485130.1685710506450.5027743744370.368259997372-0.1331907783990.389377820776-0.934751122798-0.3710514092060.0112407771390.5301196591750.0606855879051-0.06820034863730.5689588178320.006480681265020.731970826164-14.368501273240.69327483141.03568065803
92.851283112120.1803934834840.9599671370957.1420993693-2.510979299444.936459251-0.03013022193491.5995859254-0.9108058305160.00654759971062-0.633525408163-0.4029851119280.2028038938780.4024535006730.9492432076670.802529829350.0160383080102-0.08520763540230.987543740688-0.1560746851320.650829262663-11.408995823729.8796748148-19.371946331
105.31753783368-1.92494266137-1.30608323933.71983593690.4047663622250.3226373218820.342821575741-1.980160818590.336588167585-0.1835221881621.11940598853-0.0222158696151-0.592482794457-0.549713530919-0.1108701847030.883110316888-0.136206699928-0.2375470632821.060272197760.2082028648220.6823578245797.8962943946930.908432878-2.36110855974
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 389 through 508 )AA389 - 5081 - 120
22chain 'A' and (resid 509 through 522 )AA509 - 522121 - 134
33chain 'A' and (resid 523 through 556 )AA523 - 556135 - 168
44chain 'A' and (resid 557 through 602 )AA557 - 602169 - 214
55chain 'B' and (resid 389 through 508 )BB389 - 5081 - 120
66chain 'B' and (resid 509 through 522 )BB509 - 522121 - 134
77chain 'B' and (resid 523 through 556 )BB523 - 556135 - 168
88chain 'B' and (resid 557 through 603 )BB557 - 603169 - 215
99chain 'A' and (resid 701 through 701 )AC701
1010chain 'B' and (resid 701 through 701 )BD701

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