4EG2

2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with Zinc and Uridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with Zinc and Uridine.

Minasov, G.Wawrzak, Z.Skarina, T.Wang, Y.Grimshaw, S.Papazisi, L.Savchenko, A.Anderson, W.F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytidine deaminase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
298Vibrio choleraeMutation(s): 0 
Gene Names: cddVC_1231
EC: 3.5.4.5
UniProt
Find proteins for Q9KSM5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KSM5 
Go to UniProtKB:  Q9KSM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KSM5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URI
Query on URI

Download Ideal Coordinates CCD File 
BA [auth F],
EA [auth G],
HA [auth H],
J [auth A],
N [auth B],
BA [auth F],
EA [auth G],
HA [auth H],
J [auth A],
N [auth B],
Q [auth C],
S [auth D],
W [auth E]
URIDINE
C9 H12 N2 O6
DRTQHJPVMGBUCF-XVFCMESISA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth F],
DA [auth G],
GA [auth H],
I [auth A],
M [auth B],
AA [auth F],
DA [auth G],
GA [auth H],
I [auth A],
M [auth B],
P [auth C],
R [auth D],
V [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth F],
FA [auth G],
K [auth A],
O [auth B],
T [auth D],
CA [auth F],
FA [auth G],
K [auth A],
O [auth B],
T [auth D],
U [auth D],
X [auth E],
Y [auth E],
Z [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.81α = 90
b = 163.73β = 97.7
c = 111.95γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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