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- PDB-5ccr: Human Cyclophilin D Complexed with Inhibitor -

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Basic information

Entry
Database: PDB / ID: 5ccr
TitleHuman Cyclophilin D Complexed with Inhibitor
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / Cyclophilin / complex / inhibitor
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 / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / 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 / cellular response to calcium ion ...mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / 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 / cellular response to calcium ion / response to ischemia / enzyme inhibitor activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cellular response to hydrogen peroxide / protein folding / mitochondrial matrix / apoptotic process / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ethyl N-[(4-aminobenzyl)carbamoyl]-L-methioninate / FORMIC ACID / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGibson, R.P. / Shore, E. / Kershaw, N. / Awais, M. / Javed, A. / Latawiec, D. / Pandalaneni, S. / Wen, L. / Berry, N. / O'Neill, P. ...Gibson, R.P. / Shore, E. / Kershaw, N. / Awais, M. / Javed, A. / Latawiec, D. / Pandalaneni, S. / Wen, L. / Berry, N. / O'Neill, P. / Sutton, R. / Lian, L.Y.
CitationJournal: To Be Published
Title: Human Cyclophilin D Complexed with Inhibitor
Authors: Gibson, R.P. / Shore, E. / Kershaw, N. / Awais, M. / Javed, A. / Latawiec, D. / Pandalaneni, S. / Wen, L. / Berry, N. / O'Neill, P. / Sutton, R. / Lian, L.Y.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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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)18,8349
Polymers17,7831
Non-polymers1,0508
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint14 kcal/mol
Surface area7110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.590, 57.590, 111.760
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-201-

K

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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 / Mutation: K133I
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) / References: UniProt: P30405, peptidylprolyl isomerase

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Non-polymers , 7 types, 128 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-4ZT / ethyl N-[(4-aminobenzyl)carbamoyl]-L-methioninate


Mass: 325.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N3O3S
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 4M potassium formate, 0.1M BIS-TRIS propane pH9, 2% w/v PEG2000mme

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.9→38.2 Å / Num. all: 15556 / Num. obs: 15556 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.054 / Rsym value: 0.018 / Net I/σ(I): 27
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 12.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BIT

2bit


Resolution: 1.9→38.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.228 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18792 799 5.2 %RANDOM
Rwork0.15468 ---
obs0.15639 14705 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 67 120 1427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191336
X-RAY DIFFRACTIONr_bond_other_d0.0020.021297
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9851781
X-RAY DIFFRACTIONr_angle_other_deg1.06932995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2825165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52823.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94315216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.209156
X-RAY DIFFRACTIONr_chiral_restr0.1190.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211487
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02307
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9270.891657
X-RAY DIFFRACTIONr_mcbond_other0.9280.894658
X-RAY DIFFRACTIONr_mcangle_it1.3811.326820
X-RAY DIFFRACTIONr_mcangle_other1.3811.326821
X-RAY DIFFRACTIONr_scbond_it2.1061.252679
X-RAY DIFFRACTIONr_scbond_other2.1031.252679
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0891.69961
X-RAY DIFFRACTIONr_long_range_B_refined5.3538.4211521
X-RAY DIFFRACTIONr_long_range_B_other5.3528.4451522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 45 -
Rwork0.145 1080 -
obs--99.65 %

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