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- PDB-2y62: Crystal structure of Leishmanial E65Q-TIM complexed with R-Glycid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y62 | ||||||
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Title | Crystal structure of Leishmanial E65Q-TIM complexed with R-Glycidol phosphate | ||||||
![]() | TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM | ||||||
![]() | ISOMERASE / FATTY ACID BIOSYNTHESIS / TRANSITION STATE ANALOGUE / GLYCOLYSIS / PENTOSE SHUNT / GLUCONEOGENESIS / ENZYME-LIGAND COMPLEX | ||||||
Function / homology | ![]() glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Venkatesan, R. / Alahuhta, M. / Pihko, P.M. / Wierenga, R.K. | ||||||
![]() | ![]() Title: High Resolution Crystal Structures of Triosephosphate Isomerase Complexed with its Suicide Inhibitors: The Conformational Flexibility of the Catalytic Glutamate in its Closed, Liganded Active Site. Authors: Venkatesan, R. / Alahuhta, M. / Pihko, P.M. / Wierenga, R.K. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135 KB | Display | ![]() |
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PDB format | ![]() | 103.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.7 KB | Display | ![]() |
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Full document | ![]() | 458.9 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y61C ![]() 2y63C ![]() 1n55S 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 27208.236 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-G3P / | ||||
#3: Chemical | ChemComp-1GP / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | 1G3P, GOP: MICROHETEROGENEITY OBSERVED. S-GLYCIDOL PHOSPHATE BECAME GLYCEROL PHOSPHATE ESTER WITH ...1G3P, GOP: MICROHETER | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 0.48 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 21% PEG6000, 0.1 M SODIUM ACETATE PH 4.5-5.5, 1MM DTT, 1MM EDTA, 1MM NAN3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8997 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→10 Å / Num. obs: 110340 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.08→1.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.6 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1N55 Resolution: 1.08→10 Å / Num. parameters: 22132 / Num. restraintsaints: 28321 / Cross valid method: FREE R-VALUE / σ(F): 0
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Refine analyze | Occupancy sum hydrogen: 1941.59 / Occupancy sum non hydrogen: 2293.29 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→10 Å
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Refine LS restraints |
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