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- PDB-2flm: Human transthyretin (TTR) complexed with bivalant amyloid inhibit... -

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Basic information

Entry
Database: PDB / ID: 2flm
TitleHuman transthyretin (TTR) complexed with bivalant amyloid inhibitor (6 carbon linker)
ComponentsTransthyretin
KeywordsHORMONE/GROWTH FACTOR / TTR / AMYLOID / TRANSTHYRETIN / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family ...Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6CA / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPalaninathan, S.K. / Kelly, J.W. / Sacchettini, J.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Synthesis and characterization of potent bivalent amyloidosis inhibitors that bind prior to transthyretin tetramerization.
Authors: Green, N.S. / Palaninathan, S.K. / Sacchettini, J.C. / Kelly, J.W.
History
DepositionJan 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: 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_special_symmetry / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0803
Polymers27,5552
Non-polymers5261
Water3,315184
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1616
Polymers55,1094
Non-polymers1,0512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8630 Å2
ΔGint-49 kcal/mol
Surface area18420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.776, 84.605, 65.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

6CA

21A-201-

6CA

31A-201-

6CA

41A-201-

6CA

51A-201-

6CA

61A-201-

6CA

71A-201-

6CA

81A-287-

HOH

91B-205-

HOH

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Components

#1: Protein Transthyretin / Prealbumin / TBPA / TTR / ATTR


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHNTR, PKNTR / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-6CA / 4'-{6-[4-(2-CARBOXYPHENYLAMINO)-PHENOXY]-HEXYLOXY}-BIPHENYL-4-CARBOXYLIC ACID


Mass: 525.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H31NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Sep 11, 2002
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→22.19 Å / Num. all: 29034 / Num. obs: 29034 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.645→1.688 Å / % possible all: 93.92

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMZ

1bmz


Resolution: 1.65→22.19 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.086 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23396 2894 10 %RANDOM
Rwork0.19806 ---
all0.20167 29034 --
obs0.20167 26140 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2--0.51 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.65→22.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 39 184 1991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221867
X-RAY DIFFRACTIONr_bond_other_d0.0030.021680
X-RAY DIFFRACTIONr_angle_refined_deg2.2971.9642546
X-RAY DIFFRACTIONr_angle_other_deg1.97533923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19823.68476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43815283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.589158
X-RAY DIFFRACTIONr_chiral_restr0.1410.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022051
X-RAY DIFFRACTIONr_gen_planes_other00.02373
X-RAY DIFFRACTIONr_nbd_refined0.2440.2314
X-RAY DIFFRACTIONr_nbd_other0.2270.21566
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2894
X-RAY DIFFRACTIONr_nbtor_other0.0990.21122
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3580.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1461.51414
X-RAY DIFFRACTIONr_mcbond_other0.5341.5461
X-RAY DIFFRACTIONr_mcangle_it2.59621859
X-RAY DIFFRACTIONr_scbond_it4.0443850
X-RAY DIFFRACTIONr_scangle_it5.5974.5687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.645→1.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 211 -
Rwork0.263 1797 -
obs--93.92 %

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