6PHM | pdb_00006phm

Crystal structure of glucagon analog fully composed of D-amino acids in space group I41 at 1.1 A resolution

• PDB DOI: https://doi.org/10.2210/pdb6PHM/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2019-06-25 Released: 2020-07-01 
• Deposition Author(s): Mroz, P.A., Gonzalez-Gutierrez, G., DiMarchi, R.D.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.167 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

High resolution X-ray structure of glucagon and selected stereo-inversed analogs in novel crystallographic packing arrangement.

Mroz, P.A., Gonzalez-Gutierrez, G., DiMarchi, R.D.

To be published.

Biological Assembly 1  

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 3.58 kDa 
• Atom Count: 313 
• Modeled Residue Count: 28 
• Deposited Residue Count: 29 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-glucagon	A	29	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  15 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL	A	D-PEPTIDE LINKING	C3 H7 N O2		--
DAR	A	D-PEPTIDE LINKING	C6 H15 N4 O2		--
DAS	A	D-PEPTIDE LINKING	C4 H7 N O4		--
DGN	A	D-PEPTIDE LINKING	C5 H10 N2 O3		--
DHI	A	D-PEPTIDE LINKING	C6 H10 N3 O2		--
DLE	A	D-PEPTIDE LINKING	C6 H13 N O2		--
DLY	A	D-PEPTIDE LINKING	C6 H14 N2 O2		--
DPN	A	D-PEPTIDE LINKING	C9 H11 N O2		--
DSG	A	D-PEPTIDE LINKING	C4 H8 N2 O3		--
DSN	A	D-PEPTIDE LINKING	C3 H7 N O3		--
DTH	A	D-PEPTIDE LINKING	C4 H9 N O3		--
DTR	A	D-PEPTIDE LINKING	C11 H12 N2 O2		--
DTY	A	D-PEPTIDE LINKING	C9 H11 N O3		--
DVA	A	D-PEPTIDE LINKING	C5 H11 N O2		--
MED	A	D-PEPTIDE LINKING	C5 H11 N O2 S		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.167 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.37	α = 90
b = 42.37	β = 90
c = 28.74	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Mroz, P.A., Gonzalez-Gutierrez, G., DiMarchi, R.D.

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Funding Organization	Location	Grant Number
Other government	United States	Indiana University Internal grant

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-23
  Changes: Structure summary