6P4Z

Structure of gadolinium-caged cobalt (III) insulin hexamer

• PDB DOI: https://doi.org/10.2210/pdb6P4Z/pdb

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


• Deposited: 2019-05-29 Released: 2019-06-12 
• Deposition Author(s): Tran, T.H., Taylor, S.K., Stojanovic, M.N., Tong, L.
• Funding Organization(s): National Institutes of Health/National Library of Medicine (NIH/NLM)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Literature

Insulin Hexamer-Caged Gadolinium Ion as MRI Contrast-o-phore

Taylor, S.K., Tran, T.H., Liu, M.Z., Harris, P.E., Sun, Y., Jambawalikar, S.R., Tong, L., Stojanovic, M.N.

(2018) Chembiochem 24: 10646-10652

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 11.95 kDa 
• Atom Count: 806 
• Modelled Residue Count: 98 
• Deposited Residue Count: 102 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin chain A	A, C	21	Homo sapiens	Mutation(s): 0  Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin chain B	B, D	30	Homo sapiens	Mutation(s): 0  Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GD (Subject of Investigation/LOI)	F [auth B]	GADOLINIUM ATOM Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N
CO (Subject of Investigation/LOI)	E [auth B], H [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	G [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.4	α = 90
b = 81.4	β = 90
c = 33.7	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Tran, T.H., Taylor, S.K., Stojanovic, M.N., Tong, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	--

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-06-19
  Changes: Data collection, Structure summary
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary