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- PDB-1stf: THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1stf | ||||||
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Title | THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION | ||||||
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![]() | HYDROLASE(SULFHYDRYL PROTEINASE) | ||||||
Function / homology | ![]() papain / negative regulation of peptidase activity / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / serpin family protein binding / adult locomotory behavior / proteolysis involved in protein catabolic process / negative regulation of proteolysis / tertiary granule lumen / secretory granule lumen ...papain / negative regulation of peptidase activity / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / serpin family protein binding / adult locomotory behavior / proteolysis involved in protein catabolic process / negative regulation of proteolysis / tertiary granule lumen / secretory granule lumen / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / lysosome / cysteine-type endopeptidase activity / Neutrophil degranulation / nucleolus / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Stubbs, M.T. / Laber, B. / Bode, W. | ||||||
![]() | ![]() Title: The refined 2.4 A X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction. Authors: Stubbs, M.T. / Laber, B. / Bode, W. / Huber, R. / Jerala, R. / Lenarcic, B. / Turk, V. #1: ![]() Title: Minireview: The Cystatins: Protein Inhibitors of Cysteine Proteinases Authors: Turk, V. / Bode, W. #2: ![]() Title: Mutations in the Qvvag Region of the Cysteine Proteinase Inhibitor Stefin B Authors: Jerala, R. / Trstenjak-Prebanda, M. / Kroon-Zitko, L. / Lenarcic, B. / Turk, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.4 KB | Display | ![]() |
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PDB format | ![]() | 56.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376.6 KB | Display | ![]() |
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Full document | ![]() | 380.3 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO E 152 2: VAL I 66 - GLY I 67 OMEGA =214.83 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
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Components
#1: Protein | Mass: 23507.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11173.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.1 % | |||||||||||||||
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Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.37 Å / Num. obs: 16084 / % possible obs: 89 % / Rmerge(I) obs: 0.102 |
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Reflection shell | *PLUS Highest resolution: 2.37 Å / Lowest resolution: 2.44 Å |
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Processing
Software | Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.37→8 Å /
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Refinement step | Cycle: LAST / Resolution: 2.37→8 Å
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Refine LS restraints |
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Software | *PLUS Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.37 Å / Lowest resolution: 8 Å / Num. reflection obs: 16033 / Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: o_angle_d / Dev ideal: 2.1 |