5H2Q | pdb_00005h2q

Crystal structure of T brucei phosphodiesterase B2 bound to compound 13e

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.200 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5H2Q

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Trypanosomal Phosphodiesterase B1 and B2 as a Potential Therapy for Human African Trypanosomiasis

Ng, P.S., Noble, C.G., Ng, F.S.B., Chew, S.H., Lim, C.C., Manoharan, V., Wan, K.F., Vachaspati, P., Kaiser, M., Ma, N.L., Gedeck, P., Kounde, C., Rao, S.P.S.

To be published.

Macromolecule Content 

  • Total Structure Weight: 78.15 kDa 
  • Atom Count: 6,108 
  • Modeled Residue Count: 657 
  • Deposited Residue Count: 674 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphodiesterase
A, B
337Trypanosoma brucei brucei TREU927Mutation(s): 0 
EC: 3.1.4
UniProt
Find proteins for Q38F42 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q38F42 
Go to UniProtKB:  Q38F42
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38F42
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LLI

Query on LLI


Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]		(4~{a}~{S},8~{a}~{R})-2-cycloheptyl-4-[4-methoxy-3-[2-(2-oxidanylideneimidazolidin-1-yl)ethoxy]phenyl]-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one
C27 H36 N4 O4
YLCZKQRIIGKMHV-FCHUYYIVSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.200 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.21α = 90
b = 97.21β = 90
c = 120.44γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Released Date: 2017-11-01 
    • Deposition Author(s): Noble, C.G.

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description