5UE1

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase in complex with adenine from Vibrio fischeri ES114


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.131 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Vibrio fischeri ES114

Filippova, E.V.Minasov, G.Shuvalova, L.Kiryukhina, O.Dubrovska, I.Grimshaw, S.Anderson, W.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
A, B
234Aliivibrio fischeri ES114Mutation(s): 0 
Gene Names: mtnNVF_2128
EC: 3.2.2.9
UniProt
Find proteins for Q5E2X3 (Aliivibrio fischeri (strain ATCC 700601 / ES114))
Explore Q5E2X3 
Go to UniProtKB:  Q5E2X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5E2X3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9DA
Query on 9DA

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
9-DEAZAADENINE
C6 H6 N4
YRVFQPBPZCRUDX-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
O [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.642α = 90
b = 72.915β = 109.6
c = 57.563γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description