3OF3

Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae

Kim, J.Ramagopal, U.A.Burley, S.K.Almo, S.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase deoD-type 1
A, B, C, D, E, F, G, H, I, J, K, L
241Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: deoD1
EC: 2.4.2.1
Find proteins for Q9KPM0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KPM0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
DIH
Query on DIH

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one
C12 H17 N4 O3
AFNHHLILYQEHKK-BDAKNGLRSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 101.375α = 90.00
b = 160.974β = 90.00
c = 188.685γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2018-12-12
    Type: Data collection, Derived calculations, Non-polymer description, Structure summary