5URT | pdb_00005urt

Insulin with proline analog DhP at position B28 in the T2 state

• PDB DOI: https://doi.org/10.2210/pdb5URT/pdb

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


• Deposited: 2017-02-12 Released: 2018-02-14 
• Deposition Author(s): Lieblich, S.A., Fang, K.Y., Tirrell, D.A.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Starting Model: experimental

Literature

Insulin with proline analog DhP at position B28 in the T2 state

Lieblich, S.A., Fang, K.Y., Tirrell, D.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 5.84 kDa 
• Atom Count: 465 
• Modeled Residue Count: 50 
• Deposited Residue Count: 51 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin Chain A	A	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	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
8LJ	B	L-PEPTIDE LINKING	C5 H7 N O2		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free:  0.142 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.120 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.955	α = 90
b = 77.955	β = 90
c = 77.955	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Lieblich, S.A., Fang, K.Y., Tirrell, D.A.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	--

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection, Derived calculations