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Open data
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Basic information
Entry | Database: PDB / ID: 5xmt | |||||||||
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Title | Plasmodium vivax SHMT bound with PLP-glycine and GS380 | |||||||||
![]() | Serine hydroxymethyltransferase | |||||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / alpha and beta protein / methyltransferase activity / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | ![]() purine nucleobase biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity ...purine nucleobase biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / methyltransferase activity / mRNA 5'-UTR binding / pyridoxal phosphate binding / methylation / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
Model details | Plasmodium vivax SHMT bound with PLP-glycine and GS362 | |||||||||
![]() | Chitnumsub, P. / Jaruwat, A. / Leartsakulpanich, U. / Schwertz, G. / Diederich, F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational Aspects in the Design of Inhibitors for Serine Hydroxymethyltransferase (SHMT): Biphenyl, Aryl Sulfonamide, and Aryl Sulfone Motifs Authors: Schwertz, G. / Frei, M.S. / Witschel, M.C. / Rottmann, M. / Leartsakulpanich, U. / Chitnumsub, P. / Jaruwat, A. / Ittarat, W. / Schafer, A. / Aponte, R.A. / Trapp, N. / Mark, K. / Chaiyen, P. / Diederich, F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 272.6 KB | Display | ![]() |
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PDB format | ![]() | 220.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 50.7 KB | Display | |
Data in CIF | ![]() | 69.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xmpC ![]() 5xmqC ![]() 5xmrC ![]() 5xmsC ![]() 5xmuC ![]() 5xmvC ![]() 4tmrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 49249.160 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-442 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PVC01_140059500, PVP01_1453700, PVT01_140059000 / Plasmid: pET17b / Production host: ![]() ![]() References: UniProt: A0A1G4H5I1, UniProt: A5K8L9*PLUS, glycine hydroxymethyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.35 % / Mosaicity: 0.432 ° |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 8.5 / Details: PEG4000, 0.06-0.12M NaCl, 0.1M Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→30 Å / Num. obs: 42088 / % possible obs: 92.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.012 / Rrim(I) all: 0.03 / Χ2: 0.872 / Net I/σ(I): 27.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4tmr Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.876 / SU B: 11.861 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.395
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.87 Å2 / Biso mean: 32.648 Å2 / Biso min: 10.22 Å2
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Refinement step | Cycle: final / Resolution: 2.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.554→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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