[English] 日本語
![](img/lk-miru.gif)
- PDB-1ukz: SUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FR... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ukz | ||||||
---|---|---|---|---|---|---|---|
Title | SUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FROM TWO STRUCTURES OF LIGATED URIDYLATE KINASE | ||||||
![]() | URIDYLATE KINASE | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() UMP/dUMP kinase activity / UMP/CMP kinase / Interconversion of nucleotide di- and triphosphates / CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase activity / UDP biosynthetic process / nucleobase-containing compound metabolic process / nucleoside diphosphate kinase activity ...UMP/dUMP kinase activity / UMP/CMP kinase / Interconversion of nucleotide di- and triphosphates / CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase activity / UDP biosynthetic process / nucleobase-containing compound metabolic process / nucleoside diphosphate kinase activity / 'de novo' pyrimidine nucleobase biosynthetic process / phosphorylation / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Mueller-Dieckmann, H.-J. / Schulz, G.E. | ||||||
![]() | ![]() 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. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 54.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 39 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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.) ![]() ![]() References: UniProt: P15700, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor |
---|---|
#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-AMP / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | THE ADP MOLECULE IS BOUND AT THE ATP-BINDING SITE AND THE AMP AT THE NMP-BINDING SITE. THE ENZYME ...THE ADP MOLECULE IS BOUND AT THE ATP-BINDING SITE AND THE AMP AT THE NMP-BINDING SITE. THE ENZYME CONTAINS AN ADP AND AN AMP MOLECULE. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.08 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 1.93 Å / Num. obs: 17480 / % possible obs: 97 % / Num. measured all: 84238 |
---|---|
Reflection shell | *PLUS Highest resolution: 1.93 Å / Lowest resolution: 1.95 Å / % possible obs: 96 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→10 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 17480 / Rfactor all: 0.196 / Highest resolution: 1.93 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.45 |