7R38

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with S-inosyl-L-homocysteine

• PDB DOI: https://doi.org/10.2210/pdb7R38/pdb

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


• Deposited: 2022-02-06 Released: 2023-02-15 
• Deposition Author(s): Saleem-Batcha, R., Popadic, D., 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: 2.05 Å
• R-Value Free: 0.219 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with S-inosyl-L-homocysteine

Saleem-Batcha, R., Popadic, D., 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: 101.34 kDa 
• Atom Count: 7,106 
• Modelled Residue Count: 842 
• Deposited Residue Count: 882 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B	441	Pyrococcus furiosus	Mutation(s): 0  Gene Names: ahcY, PF0343 EC: 3.3.1.1
UniProt
Find proteins for P50251 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P50251  Go to UniProtKB:  P50251

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	D [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SIB (Subject of Investigation/LOI)	C [auth A], E [auth B]	(2S)-2-AMINO-4-({[(2S,3S,4R,5R)-3,4-DIHYDROXY-5-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)TETRAHYDROFURAN-2-YL]METHYL}THIO)BUTANOIC ACID C14 H19 N5 O6 S VNPWVMVYUSNFAW-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.219 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.683	α = 90
b = 111.683	β = 90
c = 121.599	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Saleem-Batcha, R., Popadic, D., Andexer, J.N.

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

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description