4F0R

Crystal structure of an adenosine deaminase homolog from Chromobacterium violaceum (target NYSGRC-019589) bound Zn and 5'-Methylthioadenosine (unproductive complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an adenosine deaminase homolog from Chromobacterium violaceum (target NYSGRC-019589) bound Zn and 5'-Methylthioadenosine (unproductive complex)

Kim, J.Vetting, M.W.Sauder, J.M.Burley, S.K.Raushel, F.M.Bonanno, J.B.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-methylthioadenosine/S-adenosylhomocysteine deaminaseA447Chromobacterium violaceum ATCC 12472Mutation(s): 0 
Gene Names: CV_1032mtaD
EC: 3.5.4.28 (PDB Primary Data), 3.5.4.31 (PDB Primary Data)
UniProt
Find proteins for Q7NZ90 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757))
Explore Q7NZ90 
Go to UniProtKB:  Q7NZ90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NZ90
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTA
Query on MTA

Download Ideal Coordinates CCD File 
D [auth A]5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.152α = 90
b = 101.152β = 90
c = 88.623γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Data collection, Structure summary
  • Version 1.2: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary