3EEI

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from neisseria meningitidis in complex with methylthio-immucillin-A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from neisseria meningitidis in complex with methylthio-immucillin-A

Ho, M., Rinaldo-matthis, A., Brown, R.L., Norris, G.E., Tyler, P.C., Furneaux, R.H., Almo, S.C., Schramm, V.L.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-methylthioadenosine nucleosidase/S-adenosylhomocysteine nucleosidase
A, B
233Neisseria meningitidis serogroup BMutation(s): 0 
Gene Names: pfs
EC: 3.2.2.16 (PDB Primary Data), 3.2.2.9 (PDB Primary Data)
UniProt
Find proteins for Q9K054 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9K054 
Go to UniProtKB:  Q9K054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K054
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MTM
Query on MTM
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		(3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL
C12 H19 N5 O2 S
YLCQGEBEQIBOOJ-BOFBLULFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.359α = 90
b = 40.897β = 109.22
c = 83.612γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations