5YG0

Plasmodium vivax SHMT bound with PLP-glycine and GS657


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

to be published

Chitnumsub, P.Jaruwat, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine hydroxymethyltransferaseA, B, C442Plasmodium vivaxMutation(s): 0 
Gene Names: PVC01_140059500PVP01_1453700PVT01_140059000
EC: 2.1.2.1
UniProt
Find proteins for A5K8L9 (Plasmodium vivax (strain Salvador I))
Explore A5K8L9 
Go to UniProtKB:  A5K8L9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K8L9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8UR
Query on 8UR

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C]
2-[1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-(trifluoromethyl)phenyl]piperidin-4-yl]ethanoic acid
C25 H28 F3 N5 O3
UHPFIFHQJWKZHI-DEOSSOPVSA-N
 Ligand Interaction
PLG
Query on PLG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
I [auth C]
N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
C10 H15 N2 O7 P
FEVQWBMNLWUBTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.248 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.561α = 90
b = 58.615β = 90.02
c = 233.052γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release