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- PDB-1tlm: STRUCTURAL ASPECTS OF INOTROPIC BIPYRIDINE BINDING: CRYSTAL STRUC... -

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Basic information

Entry
Database: PDB / ID: 1tlm
TitleSTRUCTURAL ASPECTS OF INOTROPIC BIPYRIDINE BINDING: CRYSTAL STRUCTURE DETERMINATION TO 1.9 ANGSTROMS OF THE HUMAN SERUM TRANSTHYRETIN-MILRINONE COMPLEX
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT(THYROXINE)
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/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
MILRINONE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWojtczak, A. / Luft, J. / Cody, V.
Citation
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.
#1: 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.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystal Structure Determination at 2.3 Angstroms Resolution of Human Transthyretin-3', 5'-Dibromo-2',4,4',6-Tetrahydroxyaurone Complex
Authors: Ciszak, E. / Cody, V. / Luft, J.R.
#3: Journal: Nature / Year: 1977
Title: Protein-DNA and Protein-Hormone Interactions in Prealbumin, a Model of the Thyroid Hormone Nuclear Receptor (Query)
Authors: Blake, C.C.F. / Oatley, S.J.
#6: Journal: J.Mol.Biol. / Year: 1974
Title: Structure of Human Plasma Prealbumin at 2.5 Angstroms 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.A. / Rerat, C. / Rerat, B.
#7: Journal: J.Mol.Biol. / Year: 1971
Title: An X-Ray Study of the Subunit Structure of Prealbumin
Authors: Blake, C.C.F. / Swan, I.D.A. / Rerat, C. / Berthou, J. / Laurent, A. / Rerat, B.
#4: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
Authors: Feldmann, R.J.
#5: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
Authors: Dayhoff, M.O.
History
DepositionDec 22, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 700SHEET THE FIRST STRAND OF THE *EXTERNAL* SHEET IN EACH SUBUNIT IS DISCONTINUOUS. TO ACCOMMODATE ...SHEET THE FIRST STRAND OF THE *EXTERNAL* SHEET IN EACH SUBUNIT IS DISCONTINUOUS. TO ACCOMMODATE THESE DISCONTINUITIES EACH *EXTERNAL* SHEET IS REPRESENTED HERE TWICE, WITH A DIFFERENT STRAND 1 IN EACH CASE. STRANDS 2, 3, 4 OF *X1A* ARE IDENTICAL TO STRANDS 2, 3, 4 OF *X2A*. SIMILARLY STRANDS 2, 3, 4 OF *X1B* ARE IDENTICAL TO STRANDS 2, 3, 4 OF *X2B*. THIS DESCRIPTION IS CONSISTENT WITH THAT USED BY BLAKE AND COWORKERS FOR THE NATIVE TRANSTHYRETIN PROTEIN DATA BANK ENTRY 2PAB.

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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)27,9754
Polymers27,5532
Non-polymers4222
Water2,342130
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9508
Polymers55,1064
Non-polymers8454
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)44.178, 86.384, 66.212
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-128-

MIL

21B-128-

MIL

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Components

#1: Protein TRANSTHYRETIN


Mass: 13776.376 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02766
#2: Chemical ChemComp-MIL / MILRINONE


Mass: 211.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9N3O / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: TTHY_HUMAN SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLU 63 GLN 63

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal grow
*PLUS
Temperature: 293 K / pH: 6.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mphosphate1drop
20.25 %(w/v)1,2,3-heptanetriol1drop
3ammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.89 Å / Num. obs: 16482 / % possible obs: 79 % / Num. measured all: 46029 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 1.89 Å / Lowest resolution: 2.01 Å / % possible obs: 36 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→8 Å
Details: THIS COORDINATE SET COMPRISES TWO CHAINS REPRESENTING TWO CHEMICALLY EQUIVALENT, BUT CRYSTALLOGRAPHICALLY DISTINCT, ENTITIES. THE OTHER HALF OF THE COMPLETE TETRAMER MAY BE GENERATED FROM ...Details: THIS COORDINATE SET COMPRISES TWO CHAINS REPRESENTING TWO CHEMICALLY EQUIVALENT, BUT CRYSTALLOGRAPHICALLY DISTINCT, ENTITIES. THE OTHER HALF OF THE COMPLETE TETRAMER MAY BE GENERATED FROM THIS DIMER BY THE APPLICATION OF THE CRYSTALLOGRAPHIC DIAD PARALLEL TO Z THROUGH THE ORIGIN OF THIS COORDINATE SYSTEM, I. E. XPRIME=-X, YPRIME=-Y, ZPRIME=Z.
RfactorNum. reflection
obs0.173 16162
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 32 130 2040
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_d0.060.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.21.75
X-RAY DIFFRACTIONp_mcangle_it3.432.5
X-RAY DIFFRACTIONp_scbond_it2.991.75
X-RAY DIFFRACTIONp_scangle_it4.662.5
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.20.15
X-RAY DIFFRACTIONp_singtor_nbd0.20.5
X-RAY DIFFRACTIONp_multtor_nbd0.250.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.240.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.95
X-RAY DIFFRACTIONp_staggered_tor2015
X-RAY DIFFRACTIONp_orthonormal_tor15.715
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 16162 / σ(F): 2 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS

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