4EJM

Crystal structure of a putative zinc-binding dehydrogenase (Target PSI-012003) from Sinorhizobium meliloti 1021 bound to NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a putative zinc-binding dehydrogenase (target nysgrc-012003) from sinorhizobium meliloti 1021 bound to NADP

Sampathkumar, P.Banu, N.Bhosle, R.Bonanno, J.Chamala, S.Chowdhury, S.Fiser, A.Gizzi, A.Glenn, A.S.Hammonds, J.Hillerich, B.Khafizov, K.Love, J.D.Matikainen, B.Patskovsky, Y.Seidel, R.Toro, R.Zencheck, W.Almo, S.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative zinc-binding dehydrogenase
A
370Rhizobium meliloti (strain 1021)Mutation(s): 0 
EC: 1.1.1.-
Find proteins for Q92PZ3 (Rhizobium meliloti (strain 1021))
Go to UniProtKB:  Q92PZ3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-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: 2.09 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 107.620α = 90.00
b = 107.620β = 90.00
c = 137.741γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description