- PDB-4tmr: Crystal structure of ternary complex of Plasmodium vivax SHMT wit... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4tmr
Title
Crystal structure of ternary complex of Plasmodium vivax SHMT with glycine and a novel pyrazolopyran 99S: methyl 5-{3-[(4S)-6-amino-5-cyano-3-methyl-4-(propan-2-yl)-2,4-dihydropyrano[2,3-c]pyrazol-4-yl]-5-cyanophenyl}thiophene-2-carboxylate .
Components
Serine hydroxymethyltransferase, putative
Keywords
TRANSFERASE/TRANSFERASE INHIBITOR / alpha and beta protein / Transferase / methyltransferase activity / Inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information
purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity ...purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleus / cytosol Similarity search - Function
The biological unit is the same as asymmetric unit
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Components
#1: Protein
Serinehydroxymethyltransferase, putative
Mass: 49249.160 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Plasmodium vivax SHMT with PLP-glycine Schiff base and a novel pyrazolopyran 99S Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Strain: Salvador I / Gene: PVX_100730 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / References: UniProt: A5K8L9
Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.86 / SU B: 15.777 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.278
3461
9.9 %
RANDOM
Rwork
0.21
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obs
0.217
34823
91.9 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK