3O4V | pdb_00003o4v

Crystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA

• PDB DOI: https://doi.org/10.2210/pdb3O4V/pdb

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


• Deposited: 2010-07-27 Released: 2010-08-11 
• Deposition Author(s): Siu, K.K.W., Howell, P.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Crystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA

Siu, K.K.W., Howell, P.L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 50.43 kDa 
• Atom Count: 3,972 
• Modeled Residue Count: 466 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MTA/SAH nucleosidase	A, B	234	Escherichia coli	Mutation(s): 0  Gene Names: mtn, pfs EC: 3.2.2.9 (PDB Primary Data), 3.2.2.16 (PDB Primary Data)
UniProt
Find proteins for P0AF12 (Escherichia coli (strain K12)) Explore P0AF12  Go to UniProtKB:  P0AF12

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4CT	C [auth A], F [auth B]	(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol C18 H20 Cl N5 O S MZZBHZOHYGEGEE-DOMZBBRYSA-N
GOL	D [auth A], E [auth A], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	I [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4CT	BindingDB:  3O4V	Kd: 4.70e-5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.6	α = 90
b = 69.09	β = 90
c = 128.31	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Siu, K.K.W., Howell, P.L.

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations