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- PDB-13iv: E. coli DaK bound to peptide PA1, structure A -

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Basic information

Entry
Database: PDB / ID: 13iv
TitleE. coli DaK bound to peptide PA1, structure A
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: 3.23 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

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)49,1334
Polymers47,6422
Non-polymers1,4922
Water23413
1
A: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5672
Polymers23,8211
Non-polymers7461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chaperone protein DnaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5672
Polymers23,8211
Non-polymers7461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.532, 115.895, 37.752
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

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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-A1DFX / peptide PA1-A / 1-[(2S)-2-cyclohexyl-2-({(2S)-2-cyclohexyl-2-[(pyrazine-2-carbonyl)amino]acetyl}amino)acetyl]-L-prolyl-L-norvalyl-L-phenylalanine


Type: peptide-like, Peptide-like / Mass: 745.907 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H55N7O7 / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002606
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Na2SO4 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-2 / Wavelength: 0.97931 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.23→33.73 Å / Num. obs: 7380 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.987 / Rpim(I) all: 0.17 / Rrim(I) all: 0.308 / Net I/σ(I): 6
Reflection shellResolution: 3.23→3.29 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.614 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 366 / CC star: 0.328 / Rrim(I) all: 1.922 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata reduction
PHENIX1.20.1_4487refinement
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.23→31.63 Å / SU ML: 0.4851 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.5393
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2961 363 4.93 %
Rwork0.2495 7001 -
obs0.2519 7364 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.93 Å2
Refinement stepCycle: LAST / Resolution: 3.23→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 108 13 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393343
X-RAY DIFFRACTIONf_angle_d0.80144524
X-RAY DIFFRACTIONf_chiral_restr0.05546
X-RAY DIFFRACTIONf_plane_restr0.0062596
X-RAY DIFFRACTIONf_dihedral_angle_d8.7384481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.23-3.70.36751150.30622284X-RAY DIFFRACTION99.75
3.7-4.660.28171320.23332293X-RAY DIFFRACTION99.75
4.66-31.630.28161160.23852424X-RAY DIFFRACTION99.18
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)
12.17800441980.1007930172180.6763751734562.26390531096-1.42611137821.91640847273-0.0357897387624-0.129648567768-0.3938142461980.5629357494420.183941235250.395949795731-0.254638654699-0.411044860456-0.1142632279080.546718864511-0.02593867881890.1328788269690.7066882512690.0437224351690.490691153583-17.309243904238.0408295801-4.44002870601
27.12675697197-1.914644878790.9376888572470.546230694657-0.2035645366520.113818631507-0.248168263777-0.7996997198460.5093429610840.771591074098-0.618597181792-0.0541265924808-0.924162119614-0.3308009878620.2796966862581.797504348790.0893739457269-0.06368440435460.79262538958-0.1854052544710.538077395375-8.951627089554.92624664734.76869072649
32.80350055259-1.69590436939-0.7385868347086.978881930831.611267185811.904034317760.16886188516-0.185568095082-1.459860245490.27414301691-0.283728695839-0.78039428142-0.465563893628-0.347724927885-0.07749841686830.64432736012-0.0878843379836-0.1943042896630.5574850333150.04203252497441.035455457842.2928305236825.43857646790.863155766681
42.07640557473-0.502303462940.04208154279010.874779118685-0.6313265309660.5264711417180.0807261152613-0.418696546385-1.24150609706-0.3550467341960.143056664941-0.5723701366920.1080492570030.41407092176-0.03940373933930.876124495943-0.133457666467-0.392324770850.6659506181140.2117512312171.274313149289.2010488163517.87323985844.01235264346
52.32193338890.9296197601770.7208682809872.567669360220.3306990282961.890782404640.195390363788-0.390126373664-1.04896076971-0.0264724862068-0.0537613580608-1.12153868930.186643366221-0.13632588809-0.1010136074440.5207162820790.0475312353376-0.02712965238640.6260106091880.1945057157290.82524120993115.518179642536.982135976-12.4687365802
66.712985903852.01423955733.212977806714.063142683250.4564945503561.653263257380.1123278880290.2043179820160.616500397891-0.314708693088-0.204747643028-0.207298334903-0.9303277216310.5617645294690.1874252131731.34995917334-0.2056466314860.2613344030640.861821747935-0.07339714143650.6045811463968.4108212555154.5793537436-21.9767040229
70.7728662514691.18923017413-0.4481269767825.58288535272-0.6111823219780.0109640409281-0.1348698268920.631166823803-0.8338442352850.543338766776-0.2246596541020.272890819278-0.1589308745690.3736004642790.1068898789871.091314216240.0364715254012-0.4780250624390.4751629805010.1736810160890.717203663291-5.1007682048926.6731680055-17.6265378985
83.00173360091-0.581403039431-0.6279151649822.268759870460.7015762606794.201019392250.2867228156330.33687993565-1.23226758512-0.280745573748-0.5757070400831.359939645630.5332152780160.01888399842390.1958908947810.772217604146-0.0237385974996-0.3562586317820.664011333252-0.07543048893351.07703044618-12.408964632918.6715126413-20.0542891595
94.66405967314-0.6772804444310.1264570490073.766627415661.245685444640.4333464969830.214538920012-0.233422846168-0.11960982972-0.6468182833240.2174471577930.145132710194-0.008819631615160.0583871629925-0.1832684641430.725883041821-0.2309793423850.1984711727010.98948075701-0.01624575167990.792943349674-9.6189299434630.1058086816-6.67780406581
105.602677335880.951887424720.04958154092233.83910922697-1.035333140520.7100408685760.300976056616-0.6471936106950.2543196273190.629615086196-0.302339348897-0.04037009847460.183063783117-0.07598491488340.05916782851180.7290615072240.352941285091-0.2739275907090.5567730133011.020739676741.644432214567.0100092887429.7419634734-10.3567618702
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 604 )AA557 - 604169 - 216
55chain 'B' and (resid 389 through 508 )BC389 - 5081 - 120
66chain 'B' and (resid 509 through 522 )BC509 - 522121 - 134
77chain 'B' and (resid 523 through 556 )BC523 - 556135 - 168
88chain 'B' and (resid 557 through 606 )BC557 - 606169 - 218
99chain 'A' and (resid 701 through 701 )AB701
1010chain 'B' and (resid 701 through 701 )BD701

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