9V16 | pdb_00009v16

Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant in complex with AMP

• PDB DOI: https://doi.org/10.2210/pdb9V16/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-05-19 Released: 2026-02-18 
• Deposition Author(s): Takai, M., Shobu, K., Fukuda, Y., Inoue, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria

Shobu, K., Takai, M., Tanino, H., Fukuda, Y., Inoue, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 375.9 kDa 
• Atom Count: 25,769 
• Modeled Residue Count: 3,175 
• Deposited Residue Count: 3,268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase	A, B, C, D	817	Escherichia coli K-12	Mutation(s): 2  Gene Names: glgP, glgY, b3428, JW3391 EC: 2.4.1.1
UniProt
Find proteins for P0AC86 (Escherichia coli (strain K12)) Explore P0AC86  Go to UniProtKB:  P0AC86

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.604	α = 90
b = 185.604	β = 90
c = 451.242	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-18 
Deposition Author(s): Takai, M., Shobu, K., Fukuda, Y., Inoue, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2026-02-18
  Type: Initial release