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- PDB-11pa: Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP AB -

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Basic information

Entry
Database: PDB / ID: 11pa
TitleCrystal Structure of M. tuberculosis ClpP1P2 bound to ADEP AB
Components(ATP-dependent Clp protease proteolytic subunit ...) x 2
KeywordsANTIBIOTIC / peptidase / protease / mycobacteria / tuberculosis / acyldepsipeptide / proteostasis
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / proteolysis / plasma membrane / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
: / BENZOIC ACID / : / LEUCINE / ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBurnside, C.M. / Fei, F. / Schmitz, K.R. / Sello, J.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI171196 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM133395 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI123400 United States
CitationJournal: J.Med.Chem. / Year: 2026
Title: Structural and Mechanistic Studies of ADEPs Yield Potent Antibacterials and a Drug Formulation Strategy for Tuberculosis.
Authors: Fei, F. / Burnside, C.M. / Lun, S. / Wee, D. / Kaur, M. / Anderson, H.R. / McCarroll, M.N. / Richardson, A.E. / Neglia, S. / Liu, H.M. / Wang, X. / Gupta, S. / Rhee, K.Y. / Wright, G.D. / ...Authors: Fei, F. / Burnside, C.M. / Lun, S. / Wee, D. / Kaur, M. / Anderson, H.R. / McCarroll, M.N. / Richardson, A.E. / Neglia, S. / Liu, H.M. / Wang, X. / Gupta, S. / Rhee, K.Y. / Wright, G.D. / Bryson, B.D. / Oehlers, S.H. / Bishai, W.R. / Schmitz, K.R. / Sello, J.K.
History
DepositionMar 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 1
I: ATP-dependent Clp protease proteolytic subunit 1
J: ATP-dependent Clp protease proteolytic subunit 1
K: ATP-dependent Clp protease proteolytic subunit 1
L: ATP-dependent Clp protease proteolytic subunit 1
M: ATP-dependent Clp protease proteolytic subunit 1
N: ATP-dependent Clp protease proteolytic subunit 1
O: ATP-dependent Clp protease proteolytic subunit 2
P: ATP-dependent Clp protease proteolytic subunit 2
Q: ATP-dependent Clp protease proteolytic subunit 2
R: ATP-dependent Clp protease proteolytic subunit 2
S: ATP-dependent Clp protease proteolytic subunit 2
T: ATP-dependent Clp protease proteolytic subunit 2
U: ATP-dependent Clp protease proteolytic subunit 2
V: ATP-dependent Clp protease proteolytic subunit 1
W: ATP-dependent Clp protease proteolytic subunit 1
X: ATP-dependent Clp protease proteolytic subunit 1
Y: ATP-dependent Clp protease proteolytic subunit 1
Z: ATP-dependent Clp protease proteolytic subunit 1
a: ATP-dependent Clp protease proteolytic subunit 1
b: ATP-dependent Clp protease proteolytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)643,94192
Polymers627,03128
Non-polymers16,91064
Water3,441191
1
A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 1
I: ATP-dependent Clp protease proteolytic subunit 1
J: ATP-dependent Clp protease proteolytic subunit 1
K: ATP-dependent Clp protease proteolytic subunit 1
L: ATP-dependent Clp protease proteolytic subunit 1
M: ATP-dependent Clp protease proteolytic subunit 1
N: ATP-dependent Clp protease proteolytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,04048
Polymers313,51514
Non-polymers8,52434
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57870 Å2
ΔGint-288 kcal/mol
Surface area90130 Å2
MethodPISA
2
O: ATP-dependent Clp protease proteolytic subunit 2
P: ATP-dependent Clp protease proteolytic subunit 2
Q: ATP-dependent Clp protease proteolytic subunit 2
R: ATP-dependent Clp protease proteolytic subunit 2
S: ATP-dependent Clp protease proteolytic subunit 2
T: ATP-dependent Clp protease proteolytic subunit 2
U: ATP-dependent Clp protease proteolytic subunit 2
V: ATP-dependent Clp protease proteolytic subunit 1
W: ATP-dependent Clp protease proteolytic subunit 1
X: ATP-dependent Clp protease proteolytic subunit 1
Y: ATP-dependent Clp protease proteolytic subunit 1
Z: ATP-dependent Clp protease proteolytic subunit 1
a: ATP-dependent Clp protease proteolytic subunit 1
b: ATP-dependent Clp protease proteolytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,90144
Polymers313,51514
Non-polymers8,38630
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57380 Å2
ΔGint-239 kcal/mol
Surface area89380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.120, 182.321, 188.777
Angle α, β, γ (deg.)90.000, 94.895, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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ATP-dependent Clp protease proteolytic subunit ... , 2 types, 28 molecules ABCDEFGOPQRSTUHIJKLMNVWXYZab

#1: Protein
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


Mass: 23721.990 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: mature M. tuberculosis ClpP2 with a C-terminal 6xHis tag
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: clpP2, Rv2460c, MTV008.16c / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566 / Variant (production host): delta-clpP / References: UniProt: P9WPC3, endopeptidase Clp
#2: Protein
ATP-dependent Clp protease proteolytic subunit 1 / Endopeptidase Clp 1


Mass: 21065.934 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: mature M. tuberculosis ClpP1
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: clpP1, clpP, Rv2461c, MTV008.17c / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566 / Variant (production host): delta-clpP / References: UniProt: P9WPC5, endopeptidase Clp

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Non-polymers , 6 types, 255 molecules

#3: Chemical
ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical...
ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C6H13NO2
#5: Chemical
ChemComp-A1C97 / 3,5-difluoro-N-[(5R,6aS,8R,10R,12S,13S,15aS,19S,21S,23aS)-8-fluoro-13,21-dimethyl-6,11,15,20,23-pentaoxooctadecahydro-2H,6H,11H,15H-pyrido[2,1-i]dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13]oxatetraazacyclohexadecin-12-yl]-Nalpha-[(2E,5S)-5-methylhept-2-enoyl]-L-phenylalaninamide


Mass: 802.879 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C40H53F3N6O8 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 mixture of reservoir (0.1M Bis-Tris (pH 6.5), 15% PEG3350, 0.2M sodium citrate, 10% ethylene glycol) and protein solution (3.75 mg/mL ClpP1, 3.75 mg/mL ClpP2, 0.83 mM ADEP, 0.83 mM Bz- ...Details: 1:1 mixture of reservoir (0.1M Bis-Tris (pH 6.5), 15% PEG3350, 0.2M sodium citrate, 10% ethylene glycol) and protein solution (3.75 mg/mL ClpP1, 3.75 mg/mL ClpP2, 0.83 mM ADEP, 0.83 mM Bz-Leu-Leu, 10 mM HEPES (pH 7.5), 50 mM NaCl, 4.5% DMSO)

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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: 0.92 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2025
Details: horizontal bounce Si(111) double crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 210276 / % possible obs: 98.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 49.97 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.087 / Rrim(I) all: 0.211 / Χ2: 0.931 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.75-2.85.21.3990530.4230.7710.6471.5390.82397.6
2.8-2.855.31.37391150.4720.8010.6391.520.83198
2.85-2.95.41.18490530.5680.8510.551.3090.84598.2
2.9-2.965.51.06491410.6270.8780.4931.1760.85698.2
2.96-3.035.60.91290470.7070.910.4171.0060.88898
3.03-3.15.60.85190800.7450.9240.3890.9380.90798.1
3.1-3.175.60.72291660.810.9460.3330.7980.91498.1
3.17-3.265.40.58690350.8610.9620.2780.6510.95197.9
3.26-3.365.30.47789890.9020.9740.2280.5310.96697.1
3.36-3.465.30.39991300.9330.9820.190.4440.98898.3
3.46-3.595.80.33191900.9610.990.1480.3640.98998.6
3.59-3.735.50.25891100.9710.9930.120.2861.00798.2
3.73-3.95.60.20890820.980.9950.0960.231.01997.7
3.9-4.116.20.15791980.990.9970.0670.1711.00398.6
4.11-4.366.10.12291940.9930.9980.0530.1331.00998.9
4.36-4.760.191040.9950.9990.0440.110.97398.2
4.7-5.175.70.09392680.9950.9990.0430.1030.91798.9
5.17-5.926.30.09392500.9960.9990.040.1010.87699.3
5.92-7.4670.07492790.9980.9990.030.0790.89799.2
7.46-506.60.0492450.99910.0170.0430.94897.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→49.05 Å / SU ML: 0.4054 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.4914
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2389 10733 5.1 %
Rwork0.194 199543 -
obs0.1963 210276 58.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.4 Å2
Refinement stepCycle: LAST / Resolution: 2.75→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39652 0 1156 191 40999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006341459
X-RAY DIFFRACTIONf_angle_d0.889756192
X-RAY DIFFRACTIONf_chiral_restr0.06286550
X-RAY DIFFRACTIONf_plane_restr0.01447274
X-RAY DIFFRACTIONf_dihedral_angle_d17.260615164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.780.40641210.3581933X-RAY DIFFRACTION16.97
2.78-2.810.37821190.34132259X-RAY DIFFRACTION19.84
2.81-2.850.39191360.33142547X-RAY DIFFRACTION22.19
2.85-2.880.38041400.33122968X-RAY DIFFRACTION25.76
2.88-2.920.40691940.3283398X-RAY DIFFRACTION30.15
2.92-2.960.32152320.32584078X-RAY DIFFRACTION35.53
2.96-30.3292550.33064490X-RAY DIFFRACTION39.54
3-3.050.38062480.33384876X-RAY DIFFRACTION42.59
3.05-3.10.36992660.34765111X-RAY DIFFRACTION44.59
3.1-3.150.36162810.34965231X-RAY DIFFRACTION45.52
3.15-3.20.34582520.30835336X-RAY DIFFRACTION46.77
3.2-3.260.36653100.30645345X-RAY DIFFRACTION46.96
3.26-3.320.34543130.28995363X-RAY DIFFRACTION47.19
3.32-3.390.31033300.27955432X-RAY DIFFRACTION47.51
3.39-3.460.31753140.27215540X-RAY DIFFRACTION48.83
3.46-3.550.31253270.25625834X-RAY DIFFRACTION50.92
3.55-3.630.28632950.23256033X-RAY DIFFRACTION53.09
3.63-3.730.26783690.2126211X-RAY DIFFRACTION54.72
3.73-3.840.24283590.19216784X-RAY DIFFRACTION59.03
3.84-3.970.21064290.16537682X-RAY DIFFRACTION67.19
3.97-4.110.20374840.15748378X-RAY DIFFRACTION74.02
4.11-4.270.1884980.15269113X-RAY DIFFRACTION80.41
4.27-4.470.18355470.144110083X-RAY DIFFRACTION87.53
4.47-4.70.19085410.139510346X-RAY DIFFRACTION91.02
4.7-50.21815250.151110849X-RAY DIFFRACTION94.48
5-5.380.22835240.168611043X-RAY DIFFRACTION95.79
5.38-5.920.25885590.182310995X-RAY DIFFRACTION96.14
5.92-6.780.23286030.181810905X-RAY DIFFRACTION95.58
6.78-8.530.19135840.160911064X-RAY DIFFRACTION96.86
8.53-49.050.18765780.162510316X-RAY DIFFRACTION90.34

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