8WLW

Crystal structure of DelP123_Msd in complex with 5-azauracil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.209 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.191 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted WHCClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Crystal structure of DelP123_Msd in complex with 5-azauracil

Porathoor, S.Anand, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CMP/dCMP deaminase, zinc-binding proteinA,
B [auth C],
C [auth B],
D
157Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEI_3493
UniProt
Find proteins for A0QY90 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QY90 
Go to UniProtKB:  A0QY90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QY90
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WHC (Subject of Investigation/LOI)
Query on WHC

Download Ideal Coordinates CCD File 
E [auth A],
H [auth C],
L [auth B],
O [auth D]
1~{H}-1,3,5-triazine-2,4-dione
C3 H3 N3 O2
GEWRKGDRYZIFNP-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth C],
J [auth C],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
K [auth C],
N [auth B],
P [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.209 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.191 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.75α = 90
b = 85.3β = 102.491
c = 76.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted WHCClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/HRD/NWBA/39/03/2018-19

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release