4RZ7 | pdb_00004rz7

Crystal Structure of PVX_084705 with bound PCI32765

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.238 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

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This is version 1.5 of the entry. See complete history. 

Literature

Crystal Structure of PVX_084705 with bound PCI32765

Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., He, H., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Hutchinson, A., El Bakkouri, M., Amani, M.

To be published.

Macromolecule Content 

  • Total Structure Weight: 97.17 kDa 
  • Atom Count: 6,491 
  • Modeled Residue Count: 801 
  • Deposited Residue Count: 847 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cGMP-dependent protein kinase, putative847Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PVX_084705
EC: 2.7.11.12
UniProt
Find proteins for A5K0N4 (Plasmodium vivax (strain Salvador I))
Explore A5K0N4 
Go to UniProtKB:  A5K0N4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K0N4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1E8

Query on 1E8


Download:Ideal Coordinates CCD File
B [auth A]1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one
C25 H24 N6 O2
XYFPWWZEPKGCCK-GOSISDBHSA-N
UNX

Query on UNX


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
BA [auth A]
BB [auth A]
C [auth A]
AA [auth A],
AB [auth A],
BA [auth A],
BB [auth A],
C [auth A],
CA [auth A],
CB [auth A],
D [auth A],
DA [auth A],
DB [auth A],
E [auth A],
EA [auth A],
EB [auth A],
F [auth A],
FA [auth A],
FB [auth A],
G [auth A],
GA [auth A],
GB [auth A],
H [auth A],
HA [auth A],
HB [auth A],
I [auth A],
IA [auth A],
IB [auth A],
J [auth A],
JA [auth A],
JB [auth A],
K [auth A],
KA [auth A],
KB [auth A],
L [auth A],
LA [auth A],
LB [auth A],
M [auth A],
MA [auth A],
MB [auth A],
N [auth A],
NA [auth A],
NB [auth A],
O [auth A],
OA [auth A],
OB [auth A],
P [auth A],
PA [auth A],
PB [auth A],
Q [auth A],
QA [auth A],
R [auth A],
RA [auth A],
S [auth A],
SA [auth A],
T [auth A],
TA [auth A],
U [auth A],
UA [auth A],
V [auth A],
VA [auth A],
W [auth A],
WA [auth A],
X [auth A],
XA [auth A],
Y [auth A],
YA [auth A],
Z [auth A],
ZA [auth A]
UNKNOWN ATOM OR ION
X

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.238 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.556α = 90
b = 117.422β = 95.26
c = 68.219γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
APSdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Non-polymer description
  • Version 1.2: 2015-06-24
    Changes: Database references, Structure summary
  • Version 1.3: 2015-07-22
    Changes: Structure summary
  • Version 1.4: 2017-11-22
    Changes: Advisory, Refinement description
  • Version 1.5: 2024-02-28
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary