+Open data
-Basic information
Entry | Database: PDB / ID: 8it4 | ||||||
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Title | Phosphoglycerate mutase 1 complexed with a covalent inhibitor | ||||||
Components | Phosphoglycerate mutase 1 | ||||||
Keywords | ISOMERASE/INHIBITOR / ISOMERASE-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen ...bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / Neutrophil degranulation / protein kinase binding / extracellular exosome / extracellular region / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Zhou, L. / Jiang, L.L. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Phosphoglycerate mutase 1 complexed with a covalent inhibitor Authors: Zhou, L. / Jiang, L.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8it4.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8it4.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 8it4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8it4_validation.pdf.gz | 992.3 KB | Display | wwPDB validaton report |
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Full document | 8it4_full_validation.pdf.gz | 996.6 KB | Display | |
Data in XML | 8it4_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 8it4_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/8it4 ftp://data.pdbj.org/pub/pdb/validation_reports/it/8it4 | HTTPS FTP |
-Related structure data
Related structure data | 7xb7C 7xb8C 7xb9C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29901.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1 / Production host: Escherichia coli (E. coli) References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase #2: Chemical | ChemComp-CL / | #3: Chemical | Mass: 487.954 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14ClNO7S3 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG3350, 100mM MES6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 23052 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 0.976 / CC star: 0.994 / Rmerge(I) obs: 0.287 / Rpim(I) all: 0.087 / Rrim(I) all: 0.3 / Χ2: 0.577 / Net I/σ(I): 2.9 / Num. measured all: 260646 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→36.03 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.42 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→36.03 Å
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Refine LS restraints |
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LS refinement shell |
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