+
Open data
-
Basic information
Entry | Database: PDB / ID: 1bdg | ||||||
---|---|---|---|---|---|---|---|
Title | HEXOKINASE FROM SCHISTOSOMA MANSONI COMPLEXED WITH GLUCOSE | ||||||
![]() | HEXOKINASE | ||||||
![]() | HEXOKINASE / PHOSPHOTRANSFERASE | ||||||
Function / homology | ![]() hexose metabolic process / hexokinase activity / hexokinase / D-glucose binding / intracellular glucose homeostasis / glycolytic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mulichak, A.M. / Garavito, R.M. | ||||||
![]() | ![]() Title: The structure of mammalian hexokinase-1. Authors: Mulichak, A.M. / Wilson, J.E. / Padmanabhan, K. / Garavito, R.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 94.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 74.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 456.7 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bg3C ![]() 1hkgS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 50510.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Sugar | ChemComp-GLC / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | RESIDUE NUMBERING IS BASED ON MAMMALIAN HEXOKINASE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 153 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MSC FOCUSSING MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.6 Å / Num. obs: 19765 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 38 |
Reflection shell | Resolution: 2.6→2.8 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 9 / % possible all: 88 |
Reflection | *PLUS Num. measured all: 113216 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 86 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HKG AND YHK PI MUTANT P152K COMPLEX WITH GLC PROVIDED BY H. BARTUNIK Resolution: 2.6→20 Å / Rfactor Rfree error: 0.01 / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.7 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 7
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|