[English] 日本語
![](img/lk-miru.gif)
- PDB-2wub: Crystal structure of HGFA in complex with the allosteric non- inh... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2wub | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of HGFA in complex with the allosteric non- inhibitory antibody Fab40.deltaTrp | |||||||||
![]() |
| |||||||||
![]() | HYDROLASE/IMMUNE SYSTEM / HYDROLASE IMMUNE SYSTEM COMPLEX / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() MET Receptor Activation / zymogen activation / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ganesan, R. / Eigenbrot, C. / Shia, S. | |||||||||
![]() | ![]() Title: Unraveling the Allosteric Mechanism of Serine Protease Inhibition by an Antibody Authors: Ganesan, R. / Eigenbrot, C. / Wu, Y. / Liang, W.C. / Shia, S. / Lipari, M.T. / Kirchhofer, D. | |||||||||
History |
| |||||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 267.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 212.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2wucC ![]() 3k2uC ![]() 2r0lS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-HEPATOCYTE GROWTH FACTOR ACTIVATOR ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 27982.635 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-GLYCOSYLATION AT ASN74 / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q04756, ![]() #2: Protein/peptide | Mass: 3962.654 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q04756, ![]() |
---|
-Antibody , 2 types, 4 molecules HRLQ
#3: Antibody | Mass: 23584.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Antibody | Mass: 23238.748 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
---|
-Sugars / Non-polymers , 2 types, 156 molecules ![](data/chem/img/HOH.gif)
#5: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #6: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 53.85 % / Description: NONE |
---|---|
Crystal grow![]() | pH: 7.5 / Details: 10% PEG 10,000, 100 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→50 Å / Num. obs: 33747 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 113.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 98.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2R0L Resolution: 2.9→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1089100.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.5973 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|