[English] 日本語
![](img/lk-miru.gif)
- PDB-7knf: 1.80A resolution structure of independent Phosphoglycerate mutase... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7knf | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 1.80A resolution structure of independent Phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (Ce-1 NHOH) | |||||||||
![]() |
| |||||||||
![]() | 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 / cytoplasm 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 | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 232.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 180.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 463.8 KB | Display | |
Data in XML | ![]() | 44 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kngC ![]() 5kgnS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 59289.102 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: 1608.708 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 NH-OH group. AcDYDYPGDHCYLYGT-NH-OH Source: (synth.) ![]() ![]() |
---|
-Non-polymers , 4 types, 760 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% (w/v) PEG 3350, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.8→48.6 Å / Num. obs: 101405 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2 / Num. measured all: 767614 / Scaling rejects: 26 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5KGN Resolution: 1.8→44.13 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 18.71 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.89 Å2 / Biso mean: 24.1408 Å2 / Biso min: 10.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→44.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
|