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- PDB-9h0s: Scaffold-ligand complex -

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Basic information

Entry
Database: PDB / ID: 9h0s
TitleScaffold-ligand complex
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / Peptidyl-prolyl cis-trans isomerase F / mitochondrial
Function / homology
Function and homology information


: / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / mitochondrial depolarization / negative regulation of oxidative phosphorylation ...: / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / mitochondrial depolarization / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / necroptotic process / apoptotic mitochondrial changes / cellular response to calcium ion / response to ischemia / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cellular response to hydrogen peroxide / protein folding / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily
Similarity search - Domain/homology
Chem-9CK / TRIETHYLENE GLYCOL / PHOSPHATE ION / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsZacharchenko, T. / Lian, L.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: To Be Published
Title: Scaffold-ligand complex
Authors: Zacharchenko, T. / Lian, L.Y.
History
DepositionOct 8, 2024Deposition site: PDBE / Processing site: PDBE
SupersessionNov 5, 2025ID: 6Y3E
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,07813
Polymers17,7831
Non-polymers1,29512
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint2 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.450, 57.450, 114.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-379-

HOH

21A-436-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidyl-prolyl cis-trans isomerase F, mitochondrial / PPIase F / Cyclophilin D / CypD / Cyclophilin F / Mitochondrial cyclophilin / CyP-M / Rotamase F


Mass: 17783.322 Da / Num. of mol.: 1 / Fragment: UNP residues 44-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Plasmid: pET28B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: P30405, peptidylprolyl isomerase

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Non-polymers , 7 types, 202 molecules

#2: Chemical ChemComp-9CK / 1-[(4-aminophenyl)methyl]-3-[2-[2-(2-bromophenyl)pyrazolidin-1-yl]-2-oxidanylidene-ethyl]urea


Mass: 432.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22BrN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.17 M Sodium acetate trihydrate,0.085 M Sodium cacodylate trihydrate pH 6.5,25.5% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.45→51.39 Å / Num. obs: 34902 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.9
Reflection shellResolution: 1.45→1.4892 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 2468 / CC1/2: 0.903 / Rpim(I) all: 0.117 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O8H

4o8h


Resolution: 1.45→51.386 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.75 / Details: One TLS group for whole chain A
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 1838 5.27 %Random selection
Rwork0.1682 ---
obs0.1697 34902 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 1.45→51.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 81 190 1511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051365
X-RAY DIFFRACTIONf_angle_d0.8511826
X-RAY DIFFRACTIONf_dihedral_angle_d14.869514
X-RAY DIFFRACTIONf_chiral_restr0.082191
X-RAY DIFFRACTIONf_plane_restr0.006234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48920.27311450.24712468X-RAY DIFFRACTION100
1.4892-1.5330.24771170.21642511X-RAY DIFFRACTION100
1.533-1.58250.26451390.19862475X-RAY DIFFRACTION100
1.5825-1.63910.23011350.18792517X-RAY DIFFRACTION100
1.6391-1.70470.20761280.17742503X-RAY DIFFRACTION100
1.7047-1.78230.19461570.17132520X-RAY DIFFRACTION100
1.7823-1.87630.17151440.1632494X-RAY DIFFRACTION100
1.8763-1.99380.21061340.16712523X-RAY DIFFRACTION100
1.9938-2.14780.18741590.16132528X-RAY DIFFRACTION100
2.1478-2.36390.19781480.15962545X-RAY DIFFRACTION100
2.3639-2.7060.20061310.16652597X-RAY DIFFRACTION100
2.706-3.40920.20121450.16832616X-RAY DIFFRACTION100
3.4092-51.3860.16851560.1552767X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.5477 Å / Origin y: -8.3654 Å / Origin z: -22.996 Å
111213212223313233
T0.2554 Å2-0.002 Å20.1415 Å2-0.1041 Å2-0.003 Å2--0.207 Å2
L1.0591 °20.1062 °2-0.3719 °2-1.4719 °2-0.3737 °2--1.3913 °2
S-0.1761 Å °0.0964 Å °-0.2107 Å °0.2028 Å °-0.0797 Å °0.1656 Å °0.2839 Å °-0.052 Å °0.1641 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 2 through 165)

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