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Yorodumi- PDB-4cm4: Crystal structure of pteridine reductase 1 (PTR1) from Trypanosom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cm4 | ||||||
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Title | Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor | ||||||
Components | (PTERIDINE REDUCTASE ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / PTR1 / SHORT-CHAIN DEHYDROGENASE/REDUCTASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | TRYPANOSOMA BRUCEI BRUCEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.81 Å | ||||||
Authors | Barrack, K.L. / Hunter, W.N. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Structure-Based Design and Synthesis of Antiparasitic Pyrrolopyrimidines Targeting Pteridine Reductase 1. Authors: Khalaf, A.I. / Huggan, J.K. / Suckling, C.J. / Gibson, C.L. / Stewart, K. / Giordani, F. / Barrett, M.P. / Wong, P.E. / Barrack, K.L. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cm4.cif.gz | 215.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cm4.ent.gz | 179.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/4cm4 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/4cm4 | HTTPS FTP |
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-Related structure data
Related structure data | 4cl8C 4cldC 4cleC 4clhC 4cloC 4clrC 4clxC 4cm1C 4cm3C 4cm5C 4cm6C 4cm7C 4cm8C 4cm9C 4cmaC 4cmbC 4cmcC 4cmeC 4cmgC 4cmiC 4cmjC 4cmkC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-PTERIDINE REDUCTASE ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 30685.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase |
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#2: Protein | Mass: 30669.791 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase |
-Non-polymers , 5 types, 729 molecules
#3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-4NR / #5: Chemical | ChemComp-GOL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | S-OXY CYSTEINE (CSX): CYSTEINE 168 MODIFIED TO S-OXY CYSTEINE IN CHAIN A |
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Sequence details | SEQUENCE CONTAINS ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.57 % / Description: NONE |
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Crystal grow | Details: RESERVOIR CONTAINED 1.7-2.7 M SODIUM ACETATE, 20-50 MM SODIUM CITRATE PH 4.5-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Sep 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→19.76 Å / Num. obs: 83224 / % possible obs: 92.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.81→1.9 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8.2 / % possible all: 77.1 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.81→19.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.2 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES WITH INSUFFICIENT ELECTRON DENSITY WERE NOT MODELED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.061 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→19.3 Å
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