8COD

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Mus musculus in complex with inosine

• PDB DOI: https://doi.org/10.2210/pdb8COD/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-27 Released: 2024-03-06 
• Deposition Author(s): Saleem-Batcha, R., Popadic, D., Koeppl, L.H., Andexer, J.N.
• Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.216 
• R-Value Work: 0.146 
• R-Value Observed: 0.149 

Starting Model: experimental

Literature

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Mus musculus in complex with inosine

Saleem-Batcha, R., Popadic, D., Koeppl, L.H., Andexer, J.N.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 101.74 kDa 
• Atom Count: 7,092 
• Modelled Residue Count: 858 
• Deposited Residue Count: 904 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B	452	Mus musculus	Mutation(s): 0  Gene Names: Ahcy EC: 3.13.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P50247 (Mus musculus) Explore P50247  Go to UniProtKB:  P50247
IMPC:  MGI:87968

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	C [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
NOS (Subject of Investigation/LOI)	D [auth A], G [auth B]	INOSINE C10 H12 N4 O5 UGQMRVRMYYASKQ-KQYNXXCUSA-N
NA	E [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.216 
• R-Value Work: 0.146 
• R-Value Observed: 0.149 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.22	α = 90
b = 102.526	β = 90
c = 173.408	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Saleem-Batcha, R., Popadic, D., Koeppl, L.H., Andexer, J.N.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	235777276/RTG1976
European Research Council (ERC)	European Union	ERC project 716966

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release