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- PDB-2roy: TRANSTHYRETIN (ALSO CALLED PREALBUMIN) COMPLEX WITH 3',5'-DINITRO... -

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Basic information

Entry
Database: PDB / ID: 2roy
TitleTRANSTHYRETIN (ALSO CALLED PREALBUMIN) COMPLEX WITH 3',5'-DINITRO-N-ACETYL-L-THYRONINE
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT / ALBUMIN / RETINOL-BINDING / VITAMIN A / AMYLOID / THYROID HORMONE / LIVER / PLASMA / CEREBROSPINAL FLUID / POLYNEUROPATHY / DISEASE MUTATION / THYROXINE / PREALBUMIN
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / molecular sequestering activity / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / molecular sequestering activity / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
3',5'-DINITRO-N-ACETYL-L-THYRONINE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsWojtczak, A. / Cody, V. / Luft, J.R. / Pangborn, W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structures of human transthyretin complexed with thyroxine at 2.0 A resolution and 3',5'-dinitro-N-acetyl-L-thyronine at 2.2 A resolution.
Authors: Wojtczak, A. / Cody, V. / Luft, J.R. / Pangborn, W.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Structural Aspects of Inotropic Bipyridine Binding. Crystal Structure Determination to 1.9 A of the Human Serum Transthyretin-Milrinone Complex
Authors: Wojtczak, A. / Luft, J.R. / Cody, V.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Mechanism of Molecular Recognition. Structural Aspects of 3,3'-Diiodo-L-Thyronine Binding to Human Serum Transthyretin
Authors: Wojtczak, A. / Luft, J. / Cody, V.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystal Structure Determination at 2.3-A Resolution of Human Transthyretin-3',5'-Dibromo-2',4,4',6-Tetrahydroxyaurone Complex
Authors: Ciszak, E. / Cody, V. / Luft, J.R.
#4: Journal: Nature / Year: 1977
Title: Protein-DNA and Protein-Hormone Interactions in Prealbumin: A Model of the Thyroid Hormone Nuclear Receptor?
Authors: Blake, C.C. / Oatley, S.J.
#7: Journal: J.Mol.Biol. / Year: 1974
Title: Structure of Human Plasma Prealbumin at 2.5 A Resolution. A Preliminary Report on the Polypeptide Chain Conformation, Quaternary Structure and Thyroxine Binding
Authors: Blake, C.C.F. / Geisow, M.J. / Swan, I.D. / Rerat, C. / Rerat, B.
#8: Journal: J.Mol.Biol. / Year: 1971
Title: An X-Ray Study of the Subunit Structure of Prealbumin
Authors: Blake, C.C. / Swan, I.D. / Rerat, C. / Berthou, J. / Laurent, A. / Rerat, B.
#5: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#6: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1976
History
DepositionOct 23, 1996Processing site: BNL
SupersessionApr 21, 1997ID: 1ROY
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3654
Polymers27,5552
Non-polymers8112
Water1,47782
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7318
Polymers55,1094
Non-polymers1,6214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9310 Å2
ΔGint-56 kcal/mol
Surface area20030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.621, 86.041, 64.953
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
11B-128-

P28

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Components

#1: Protein TRANSTHYRETIN / PREALBUMIN


Mass: 13777.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PLASMA / Tissue: PLASMA / References: UniProt: P02766
#2: Chemical ChemComp-P28 / 3',5'-DINITRO-N-ACETYL-L-THYRONINE


Mass: 405.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15N3O9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal grow
*PLUS
pH: 6.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMphosphate1drop
255 %ammonium sulfate1reservoir
30.1 Mphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 12450 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Num. measured all: 70011 / Rmerge(I) obs: 0.069

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→8 Å
Details: THE MODEL CONTAINS THE 3', 5'-DINITRO-N-ACETYL-THYRONINE MOLECULE IN BOTH BINDING SITES. THE OCCUPANCY OF 50% REFLECTS THE PRESENCE OF CRYSTALLOGRAPHIC TWO-FOLD AXIS CAUSING STATISTICAL ...Details: THE MODEL CONTAINS THE 3', 5'-DINITRO-N-ACETYL-THYRONINE MOLECULE IN BOTH BINDING SITES. THE OCCUPANCY OF 50% REFLECTS THE PRESENCE OF CRYSTALLOGRAPHIC TWO-FOLD AXIS CAUSING STATISTICAL DISORDER OF THE LIGAND, AND CORRESPONDS TO SATURATION OF THE BINDING SITES.
RfactorNum. reflection
Rwork0.184 -
obs-9664
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 58 82 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.060.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.070.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.721.75
X-RAY DIFFRACTIONp_mcangle_it2.662.5
X-RAY DIFFRACTIONp_scbond_it2.031.75
X-RAY DIFFRACTIONp_scangle_it3.12.5
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.20.15
X-RAY DIFFRACTIONp_singtor_nbd0.230.5
X-RAY DIFFRACTIONp_multtor_nbd0.30.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.330.5
X-RAY DIFFRACTIONp_planar_tor3.25
X-RAY DIFFRACTIONp_staggered_tor21.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.615
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.63 Å2

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