[English] 日本語
Yorodumi
- PDB-1bm7: HUMAN TRANSTHYRETIN (PREALBUMIN) COMPLEX WITH FLUFENAMIC ACID (2-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bm7
TitleHUMAN TRANSTHYRETIN (PREALBUMIN) COMPLEX WITH FLUFENAMIC ACID (2-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID)
ComponentsPROTEIN (TRANSTHYRETIN)
KeywordsSIGNALING PROTEIN / THYROXINE TRANSPORT
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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
2-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 Å
AuthorsKlabunde, T. / Kelly, J.W. / Sacchettini, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Inhibiting transthyretin conformational changes that lead to amyloid fibril formation.
Authors: Peterson, S.A. / Klabunde, T. / Lashuel, H.A. / Purkey, H. / Sacchettini, J.C. / Kelly, J.W.
History
DepositionJul 29, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 5, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (TRANSTHYRETIN)
B: PROTEIN (TRANSTHYRETIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1174
Polymers27,5552
Non-polymers5622
Water97354
1
A: PROTEIN (TRANSTHYRETIN)
B: PROTEIN (TRANSTHYRETIN)
hetero molecules

A: PROTEIN (TRANSTHYRETIN)
B: PROTEIN (TRANSTHYRETIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2348
Polymers55,1094
Non-polymers1,1254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)43.180, 85.320, 64.460
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-501-

FLF

21B-502-

FLF

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98541, 0.170164, 0.003243), (0.170147, 0.985406, -0.004947), (-0.004037, -0.004324, -0.999983)
Vector: 35.4085, -2.9944, 32.2167)

-
Components

#1: Protein PROTEIN (TRANSTHYRETIN) / PREALBUMIN


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: PLASMA / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-FLF / 2-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID / FLUFENAMIC ACID / Flufenamic acid


Mass: 281.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10F3NO2 / Comment: antiinflammatory, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
2100 mM1dropKCl
3100 mMphosphate1drop
41 Mammonium sulfate1drop
52 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 16664 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.063 / Rsym value: 6.3 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.285 / Rsym value: 28.5 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 86716
Reflection shell
*PLUS
% possible obs: 99.4 %

-
Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2→8 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 3
Details: THE STRUCTURE CONTAINS THE FLUFENAMIC ACID MOLECULES THAT BIND IN TWO OVERLAPPING BINDING MODES IN EACH OF TWO INDEPENDENT BINDING SITES OF THE TETRAMER. SINCE THE BINDING IS ALONG THE 2- ...Details: THE STRUCTURE CONTAINS THE FLUFENAMIC ACID MOLECULES THAT BIND IN TWO OVERLAPPING BINDING MODES IN EACH OF TWO INDEPENDENT BINDING SITES OF THE TETRAMER. SINCE THE BINDING IS ALONG THE 2-FOLD CRYSTALLOGRAPHIC AXIS, AN OCCUPANCY OF 0.25 CORRESPONDS TO SATURATION OF EACH OF THE BINDING SITES.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1528 10 %RANDOM
Rwork0.189 ---
obs0.189 15239 92.9 %-
Displacement parametersBiso mean: 29.7 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 80 54 1896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.037
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
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 0.1122 Å / Weight position: 100
LS refinement shellResolution: 2→2.03 Å / Total num. of bins used: 20
Rfactor% reflection
Rfree0.248 10 %
Rwork0.266 -
obs-85.75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2FLU_MOPAC.PARFLU_MOPAC.TOP

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more