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- PDB-1kui: Crystal Structure of a Taiwan Habu Venom Metalloproteinase comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kui | |||||||||
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Title | Crystal Structure of a Taiwan Habu Venom Metalloproteinase complexed with pEQW. | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / alpha/beta protein / retro-binding manner / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, K.F. / Chiou, S.H. / Ko, T.P. / Wang, A.H.J. | |||||||||
![]() | ![]() Title: Determinants of the inhibition of a Taiwan habu venom metalloproteinase by its endogenous inhibitors revealed by X-ray crystallography and synthetic inhibitor analogues. Authors: Huang, K.F. / Chiou, S.H. / Ko, T.P. / Wang, A.H. #1: ![]() Title: Characterization of multiple metalloproteinases with fibrinogenolytic activity from the venom of Taiwan habu (Trimeresurus mucrosquamatus): protein microsequencing coupled with cDNA sequence analysis. Authors: Huang, K.F. / Hung, C.C. / Pan, F.M. / Chow, L.P. / Tsugita, A. / Chiou, S.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.8 KB | Display | ![]() |
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PDB format | ![]() | 49.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425 KB | Display | ![]() |
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Full document | ![]() | 426.3 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23378.809 Da / Num. of mol.: 1 / Fragment: CATALYTIC PROTEASE DOMAIN / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: O57413, EC: 3.4.24.44 | ||
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#2: Protein/peptide | Mass: 443.453 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: pEQW was synthesized by solid-phase chemical method. | ||
#3: Chemical | ChemComp-CD / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.71 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG400, sodium acetate, cadmium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SIEMENS / Detector: CCD / Date: Jan 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 273510 / Num. obs: 38788 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 5.7 / Num. unique all: 3867 / % possible all: 99.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 273510 |
Reflection shell | *PLUS % possible obs: 99.4 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |