7DAH

Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae in complex with ATP and PRPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae in complex with ATP and PRPP

Pal, R.K.Gourinath, S.Biswal, B.K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP phosphoribosyltransferase
A, B, C, D, E, F
A, B, C, D, E, F
310Vibrio cholerae M66-2Mutation(s): 0 
Gene Names: hisGVCM66_1088
EC: 2.4.2.17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
M [auth C],
Z [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PRP (Subject of Investigation/LOI)
Query on PRP

Download Ideal Coordinates CCD File 
N [auth C],
Y [auth F]
1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
 Ligand Interaction
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A],
P [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
J [auth A],
U [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A],
R [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
O [auth C],
Q [auth D],
S [auth D],
H [auth A],
I [auth A],
O [auth C],
Q [auth D],
S [auth D],
T [auth D],
V [auth E],
X [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
L [auth C],
W [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.603α = 90
b = 136.603β = 90
c = 121.931γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release