[English] 日本語
![](img/lk-miru.gif)
- PDB-1lk6: Structure of dimeric antithrombin complexed with a P14-P9 reactiv... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1lk6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide | |||||||||
![]() |
| |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Loop-sheet polymer / ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhou, A. / Huntington, J.A. / Lomas, D.A. / Carrell, R.W. / Stein, P.E. | |||||||||
![]() | ![]() Title: Serpin Polymerization Is Prevented by a Hydrogen Bond Network That Is Centered on His-334 and Stabilized by Glycerol Authors: Zhou, A. / Stein, P.E. / Huntington, J.A. / Carrell, R.W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 163.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 131 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1jvqS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules LI
#1: Protein | ![]() Mass: 49101.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
---|
-Protein/peptide , 2 types, 2 molecules CD
#2: Protein/peptide | Mass: 560.556 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence ocurs naturally in human antithrombin |
---|---|
#3: Protein/peptide | Mass: 437.553 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Sugars , 2 types, 8 molecules ![](data/chem/img/NDG.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#4: Sugar | ChemComp-NDG / ![]() #5: Sugar | ![]() |
---|
-Non-polymers , 2 types, 35 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-GOL / ![]() |
---|---|
#7: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.6 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 4000, sodium cacodylate, ammonium fluoride, glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2002 / Details: mirrors |
Radiation | Monochromator: cooled liquid gallium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→37.58 Å / Num. all: 27398 / Num. obs: 27376 / % possible obs: 96.7 % / Observed criterion σ(I): -3.7 / Redundancy: 3.3 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.087 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3351 / Rsym value: 0.431 / % possible all: 81.5 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 91051 |
Reflection shell | *PLUS Lowest resolution: 2.93 Å / % possible obs: 81.5 % |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: Dimeric antithrombin complexed with a P14-P8 reactive loop peptide and an exogenous tetrapeptide (1jvq). Both peptides omitted in starting model Resolution: 2.8→34.03 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood target
| |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.26 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→34.03 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 34 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|