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Yorodumi- PDB-1uky: SUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uky | ||||||
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Title | SUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FROM TWO STRUCTURES OF LIGATED URIDYLATE KINASE | ||||||
Components | URIDYLATE KINASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information UMP/dUMP kinase activity / UMP/CMP kinase / CDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / cytidylate kinase activity / UMP kinase activity / adenylate kinase activity / UDP biosynthetic process / nucleobase-containing compound metabolic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP/dUMP kinase activity / UMP/CMP kinase / CDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / cytidylate kinase activity / UMP kinase activity / adenylate kinase activity / UDP biosynthetic process / nucleobase-containing compound metabolic process / 'de novo' pyrimidine nucleobase biosynthetic process / phosphorylation / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.13 Å | ||||||
Authors | Mueller-Dieckmann, H.-J. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase. Authors: Muller-Dieckmann, H.J. / Schulz, G.E. #1: Journal: J.Mol.Biol. / Year: 1994 Title: The Structure of Uridylate Kinase with its Substrates, Showing the Transition State Geometry Authors: Mueller-Dieckmann, H.-J. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uky.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uky.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 1uky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/1uky ftp://data.pdbj.org/pub/pdb/validation_reports/uk/1uky | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 106 |
-Components
#1: Protein | Mass: 22834.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P15700, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THE COMPLEX CONTAINS AN ADP AT THE ATP-BINDING SITE AND A MIXTURE OF ADP AND AMP AT THE NMP-BINDING SITE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.13 Å / Num. obs: 12091 / % possible obs: 91 % / Num. measured all: 32483 |
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Reflection shell | *PLUS Highest resolution: 2.13 Å / Lowest resolution: 2.19 Å / % possible obs: 64 % |
-Processing
Software |
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Refinement | Resolution: 2.13→10 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.13→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.1 |