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- PDB-1a7x: FKBP12-FK1012 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a7x
TitleFKBP12-FK1012 COMPLEX
ComponentsFKBP12
KeywordsISOMERASE / IMMUNOPHILIN
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding / regulation of amyloid precursor protein catabolic process / signaling receptor inhibitor activity / terminal cisterna / ryanodine receptor complex / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / protein maturation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / protein folding / regulation of protein localization / protein refolding / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / membrane / cytoplasm / cytosol
Similarity search - Function
Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-FKA / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchultz, L.W. / Clardy, J.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 1998
Title: Chemical inducers of dimerization: the atomic structure of FKBP12-FK1012A-FKBP12.
Authors: Schultz, L.W. / Clardy, J.
#1: Journal: Science / Year: 1991
Title: Atomic Structure of Fkbp-Fk506, an Immunophilin-Immunosuppressant Complex
Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
#2: Journal: Nature / Year: 1990
Title: Molecular Cloning and Overexpression of the Human Fk506-Binding Protein Fkbp
Authors: Standaert, R.F. / Galat, A. / Verdine, G.L. / Schreiber, S.L.
History
DepositionMar 18, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FKBP12
B: FKBP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6143
Polymers23,6732
Non-polymers9411
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.590, 40.510, 93.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-497-

HOH

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Components

#1: Protein FKBP12


Mass: 11836.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Chemical ChemComp-FKA / BENZYL-CARBAMIC ACID [8-DEETHYL-ASCOMYCIN-8-YL]ETHYL ESTER


Mass: 941.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H76N2O14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: A 10MG/ML SOLUTION OF FK1012A IN MEOH WAS ADDED IN A 1:2 MOLAR RATIO TO A 10MG/ML SOLUTION OF FKBP12 IN 10MM TRIS PH 8.2. THE SAMPLE WAS GENTLY MIXED AND ALLOWED TO INCUBATE OVERNIGHT TO ...Details: A 10MG/ML SOLUTION OF FK1012A IN MEOH WAS ADDED IN A 1:2 MOLAR RATIO TO A 10MG/ML SOLUTION OF FKBP12 IN 10MM TRIS PH 8.2. THE SAMPLE WAS GENTLY MIXED AND ALLOWED TO INCUBATE OVERNIGHT TO ENSURE COMPLETE BINDING. CRYSTALS WERE GROWN USING THE HANGING DROP METHOD WITH 0.5ML RESERVOIR CONSISTING OF 5.1M SODIUM FORMATE AND 0.1M SODIUM ACETATE PH 4.6. THE DROPS CONSISTED OF 3UL OF PROTEIN AND 3UL OF RESERVOIR SOLUTION., vapor diffusion - hanging drop
PH range: 5.1-8.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop contains equal volume of the reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMTris-HCl1drop
35.1 Msodium formate1reservoir
40.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 10, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 15896 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 0.046 / Net I/σ(I): 14
Reflection
*PLUS
Rmerge(I) obs: 0.046

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FKF

1fkf


Resolution: 2→8 Å / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 72 176 2290
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS

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