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- PDB-6ep1: Transthyretin in complex with 5-(4-nitrophenylazo)-3-iodosalicyli... -

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Basic information

Entry
Database: PDB / ID: 6ep1
TitleTransthyretin in complex with 5-(4-nitrophenylazo)-3-iodosalicylic acid
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloid inhibitor / FAP inhibitor / transthyretin
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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, 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
Similarity search - Domain/homology
5-(4-nitrophenylazo)-3-iodosalicylic acid / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLeite, J.P. / Gales, L.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Targeting transthyretin in Alzheimer's disease: Drug discovery of small-molecule chaperones as disease-modifying drug candidates for Alzheimer's disease
Authors: Leite, J.P. / Gales, L.
History
DepositionOct 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)26,0384
Polymers25,2122
Non-polymers8262
Water2,522140
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0778
Polymers50,4244
Non-polymers1,6524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)42.900, 85.270, 64.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

BQB

21A-201-

BQB

31A-201-

BQB

41A-201-

BQB

51A-201-

BQB

61B-201-

BQB

71B-201-

BQB

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 22 or resid 24...
21(chain B and (resid 10 through 22 or resid 24...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSGLYGLY(chain A and (resid 10 through 22 or resid 24...AA10 - 221 - 13
12PROPROILEILE(chain A and (resid 10 through 22 or resid 24...AA24 - 2615 - 17
13VALVALILEILE(chain A and (resid 10 through 22 or resid 24...AA28 - 8419 - 75
14PROPROTYRTYR(chain A and (resid 10 through 22 or resid 24...AA86 - 11477 - 105
15TYRTYRTHRTHR(chain A and (resid 10 through 22 or resid 24...AA116 - 118107 - 109
16ALAALAASNASN(chain A and (resid 10 through 22 or resid 24...AA120 - 124111 - 115
21CYSCYSGLYGLY(chain B and (resid 10 through 22 or resid 24...BB10 - 221 - 13
22PROPROILEILE(chain B and (resid 10 through 22 or resid 24...BB24 - 2615 - 17
23VALVALILEILE(chain B and (resid 10 through 22 or resid 24...BB28 - 8419 - 75
24PROPROTYRTYR(chain B and (resid 10 through 22 or resid 24...BB86 - 11477 - 105
25TYRTYRTHRTHR(chain B and (resid 10 through 22 or resid 24...BB116 - 118107 - 109
26ALAALAASNASN(chain B and (resid 10 through 22 or resid 24...BB120 - 124111 - 115

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12606.103 Da / Num. of mol.: 2 / Fragment: UNP Residues 30-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02766
#2: Chemical ChemComp-BQB / 5-(4-nitrophenylazo)-3-iodosalicylic acid


Mass: 413.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8IN3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.34 Å3/Da / Density % sol: 47.5 % / Mosaicity: 0.2 °
Crystal growTemperature: 293 K / Method: evaporation
Details: acetate buffer 0.2 M pH 4.8-5.4, ammonium sulfate 1.8-2.2 M, 7% glycerol
PH range: 4.8-5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.269→51.487 Å / Num. obs: 61714 / % possible obs: 97.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 14.43 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.085 / Rsym value: 0.077 / Net I/av σ(I): 3.3 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.27-1.345.70.970.486560.4431.0690.9795.1
1.34-1.425.80.6580.583090.2970.7230.65896.4
1.42-1.525.90.440.878880.1960.4830.4496.9
1.52-1.645.80.2551.473890.1140.280.25597.6
1.64-1.795.90.1682.268480.0740.1840.16897.8
1.79-2.015.90.0924.962310.0410.1010.09298.3
2.01-2.3260.0677.656040.030.0730.06799.1
2.32-2.845.90.062848040.0280.0680.06299.6
2.84-4.015.80.054937740.0240.0590.05499.8
4.01-64.595.40.0566.822110.0280.0630.05699.7

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1y1d

1y1d


Resolution: 1.3→51.487 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.59
RfactorNum. reflection% reflection
Rfree0.1895 2920 5.07 %
Rwork0.1593 --
obs0.1608 57564 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.15 Å2 / Biso mean: 21.9076 Å2 / Biso min: 9.7 Å2
Refinement stepCycle: final / Resolution: 1.3→51.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 44 140 1960
Biso mean--30.7 33.85 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051891
X-RAY DIFFRACTIONf_angle_d0.8122588
X-RAY DIFFRACTIONf_chiral_restr0.083290
X-RAY DIFFRACTIONf_plane_restr0.006329
X-RAY DIFFRACTIONf_dihedral_angle_d16.251662
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A968X-RAY DIFFRACTION8.34TORSIONAL
12B968X-RAY DIFFRACTION8.34TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.32130.25291450.2012518266396
1.3213-1.34410.21771290.19762508263795
1.3441-1.36860.24331370.17612512264996
1.3686-1.39490.20921220.16472537265996
1.3949-1.42340.19251350.15542546268196
1.4234-1.45430.18751270.14692540266796
1.4543-1.48810.1651190.13982579269897
1.4881-1.52540.17011490.13262544269397
1.5254-1.56660.15961540.13152539269397
1.5666-1.61270.16851310.12342601273297
1.6127-1.66480.1511310.1262568269997
1.6648-1.72430.16721500.13452605275598
1.7243-1.79330.19381300.13952584271497
1.7933-1.87490.18511310.13612588271997
1.8749-1.97380.14341580.12742597275598
1.9738-2.09740.16911440.13232657280199
2.0974-2.25940.15961330.13922658279199
2.2594-2.48680.18641390.16292678281799
2.4868-2.84660.18941500.18032687283799
2.8466-3.58630.21181480.170227492897100
3.5863-51.5270.2111580.18592849300799

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