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- PDB-6tx9: CRYSTAL STRUCTURE OF HUMAN FKBP51 FK1 DOMAIN A19T MUTANT IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 6tx9
TitleCRYSTAL STRUCTURE OF HUMAN FKBP51 FK1 DOMAIN A19T MUTANT IN COMPLEX WITH HYDANTOIN
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / PPIase / Fragment
Function / homology
Function and homology information


FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding ...FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. ...Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
imidazolidine-2,4-dione / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsFiegen, D. / Draxler, S.W.
Citation
Journal: J.Med.Chem. / Year: 2020
Title: Hybrid Screening Approach for Very Small Fragments: X-ray and Computational Screening on FKBP51.
Authors: Draxler, S.W. / Bauer, M. / Eickmeier, C. / Nadal, S. / Nar, H. / Rangel Rojas, D. / Seeliger, D. / Zeeb, M. / Fiegen, D.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2011
Title: Structural characterization of the PPIase domain of FKBP51, a cochaperone of human Hsp90.
Authors: Bracher, A. / Kozany, C. / Thosta, A.-K. / Hauschb, F.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1724
Polymers14,0261
Non-polymers1463
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-14 kcal/mol
Surface area7030 Å2
Unit cell
Length a, b, c (Å)42.233, 54.418, 56.73
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated ...PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase


Mass: 14026.077 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-HYN / imidazolidine-2,4-dione / Hydantoin / Hydantoin


Mass: 100.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 28-41% PEG3350, 0.2 M NH4OAc, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.415→56.73 Å / Num. obs: 25620 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Net I/σ(I): 19.6
Reflection shellResolution: 1.415→1.44 Å / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1252 / Rpim(I) all: 0.284 / % possible all: 98.7

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSMay 1, 2016data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o5q

3o5q


Resolution: 1.42→16.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.066 / SU Rfree Cruickshank DPI: 0.061
RfactorNum. reflection% reflectionSelection details
Rfree0.187 509 -RANDOM
Rwork0.162 ---
obs0.162 25545 99.9 %-
Displacement parametersBiso mean: 20.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.1144 Å20 Å20 Å2
2---0.0445 Å20 Å2
3---0.1589 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.42→16.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 9 202 1197
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011173HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.171597HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d435SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes206HARMONIC5
X-RAY DIFFRACTIONt_it1173HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion144SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1651SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.1
X-RAY DIFFRACTIONt_other_torsion14.51
LS refinement shellResolution: 1.42→1.44 Å
RfactorNum. reflection% reflection
Rfree0.2104 26 -
Rwork0.188 --
obs0.1886 1022 98.24 %
Refinement TLS params.Origin x: 9.0717 Å / Origin y: -12.3711 Å / Origin z: -9.5169 Å
111213212223313233
T-0.0052 Å2-0.0011 Å2-0.0043 Å2--0.0137 Å20.0016 Å2---0.0149 Å2
L0.7158 °2-0.194 °20.0756 °2-1.0072 °20.0083 °2--0.6001 °2
S0.0185 Å °-0.0577 Å °0.0072 Å °-0.0577 Å °0.0101 Å °0.0593 Å °0.0072 Å °0.0593 Å °-0.0286 Å °
Refinement TLS groupSelection details: { A|* }

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