5URU | pdb_00005uru

Insulin with proline analog DhP at position B28 in the R6 state

• PDB DOI: https://doi.org/10.2210/pdb5URU/pdb

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


• Deposited: 2017-02-13 Released: 2018-02-21 
• 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: 2.41 Å
• R-Value Free: 
  0.246 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Insulin with proline analog DhP at position B28 in the R6 state

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

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.04 kDa 
• Atom Count: 1,462 
• Modeled Residue Count: 194 
• Deposited Residue Count: 204 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin Chain A	A, C, E, G	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, F, H	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
IPH	I [auth A], L [auth C], O [auth E], R [auth G]	PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N
ZN	J [auth B], M [auth D], P [auth F], S [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	K [auth B], N [auth D], Q [auth F], T [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.246 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.259	α = 90
b = 79.259	β = 90
c = 79.874	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-21 
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: 2018-02-21
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection, Derived calculations