5ISY

Crystal structure of Nudix family protein with NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural basis of prokaryotic NAD-RNA decapping by NudC

Zhang, D.Liu, Y.Wang, Q.Guan, Z.Wang, J.Liu, J.Zou, T.Yin, P.

(2016) Cell Res 26: 1062-1066


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH pyrophosphataseA,
B [auth C]
259Escherichia coli K-12Mutation(s): 1 
Gene Names: nudCyjaDb3996JW5548
EC: 3.6.1.22 (PDB Primary Data), 3.6.1 (UniProt)
UniProt
Find proteins for P32664 (Escherichia coli (strain K12))
Explore P32664 
Go to UniProtKB:  P32664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32664
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
D [auth A],
F [auth C]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
E [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.411α = 90
b = 98.702β = 90
c = 113.739γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
HKL-3000data processing
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release