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- PDB-7kng: 2.10A resolution structure of independent Phosphoglycerate mutase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kng | |||||||||
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Title | 2.10A resolution structure of independent Phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (Ce-2 Y7F) | |||||||||
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![]() | ISOMERASE / phosphoglycerate mutase / ipglycermide / peptide inhibitors / metal ion binding | |||||||||
Function / homology | ![]() phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity / glucose catabolic process / glycolytic process / manganese ion binding / carbohydrate metabolic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Weidmann, M. / Dranchak, P. / Aitha, M. / Queme, B. / Collmus, C.D. / Kanter, L. / Lamy, L. ...Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Weidmann, M. / Dranchak, P. / Aitha, M. / Queme, B. / Collmus, C.D. / Kanter, L. / Lamy, L. / Tao, D. / Rai, G. / Suga, H. / Inglese, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-activity relationship of ipglycermide binding to phosphoglycerate mutases. Authors: Wiedmann, M. / Dranchak, P.K. / Aitha, M. / Queme, B. / Collmus, C.D. / Kashipathy, M.M. / Kanter, L. / Lamy, L. / Rogers, J.M. / Tao, D. / Battaile, K.P. / Rai, G. / Lovell, S. / Suga, H. / Inglese, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.7 KB | Display | ![]() |
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PDB format | ![]() | 174.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.9 KB | Display | ![]() |
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Full document | ![]() | 456.7 KB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 58.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7knfC ![]() 5kgnS 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
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 59257.102 Da / Num. of mol.: 2 / Fragment: M19 to I539 (isoform b) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: G5EFZ1, phosphoglycerate mutase (2,3-diphosphoglycerate-independent) #2: Protein/peptide | Mass: 1703.871 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Chains C and D are an N-terminal acetylated peptide with a D-Tyr at position 1. The acetylated group is covalently bound to Cys 8 to form a cyclic peptide. The peptide is terminated with an ...Details: Chains C and D are an N-terminal acetylated peptide with a D-Tyr at position 1. The acetylated group is covalently bound to Cys 8 to form a cyclic peptide. The peptide is terminated with an NH2 group. Ac(DTY)DYPGDFCYLYNH2 Source: (synth.) ![]() ![]() |
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-Non-polymers , 4 types, 411 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% (w/v) PEG 3350, 0.1 M Hepes, 3% (w/v) Trimethylamine N-oxide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 15, 2020 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→44.69 Å / Num. obs: 64166 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.105 / Net I/σ(I): 8.9 / Num. measured all: 219493 / Scaling rejects: 95 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KGN Resolution: 2.1→44.69 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 24.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.02 Å2 / Biso mean: 30.8718 Å2 / Biso min: 16.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→44.69 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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