4X30 | pdb_00004x30

Crystal structure of human Thyroxine-binding globulin complexed with thyroine at 1.55 Angstrom resolution

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2014-11-27 Released: 2015-12-02 
  • Deposition Author(s): Qi, X.
  • Funding Organization(s): National Natural Science Foundation of China, nsfc

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.205 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 

Literature

Crystal structure of human Thyroxine-binding globulin complexed with thyroine at 1.55 Angstrom resolution

Qi, X., Zhou, A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 45.21 kDa 
  • Atom Count: 3,443 
  • Modeled Residue Count: 372 
  • Deposited Residue Count: 395 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thyroxine-binding globulin395Homo sapiensMutation(s): 0 
Gene Names: SERPINA7, TBG
UniProt & NIH Common Fund Data Resources
Find proteins for P05543 (Homo sapiens)
Explore P05543 
Go to UniProtKB:  P05543
PHAROS:  P05543
GTEx:  ENSG00000123561 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05543
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T44

Query on T44


Download:Ideal Coordinates CCD File
B [auth A]3,5,3',5'-TETRAIODO-L-THYRONINE
C15 H11 I4 N O4
XUIIKFGFIJCVMT-LBPRGKRZSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA

Query on NA


Download:Ideal Coordinates CCD File
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
F

Query on F


Download:Ideal Coordinates CCD File
E [auth A]FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.205 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.46α = 90
b = 65.46β = 90
c = 202.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
MOSFLMdata processing
PHASERphasing
SCALAdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2015-12-02 
    • Deposition Author(s): Qi, X.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31170724
nsfcChina31370727

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection