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Open data
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Basic information
Entry | Database: PDB / ID: 3er3 | ||||||
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Title | The active site of aspartic proteinases | ||||||
![]() | ENDOTHIAPEPSIN | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Al-Karadaghi, S. / Cooper, J.B. / Veerapandian, B. / Hoover, D. / Blundell, T.L. | ||||||
![]() | ![]() Title: The Active Site of Aspartic Proteinases Authors: Pearl, L. / Blundell, T. #1: ![]() Title: Active Site of Acid Proteinases Authors: Blundell, T.L. / Jones, H.B. / Khan, G. / Taylor, G. / Sewell, T.S. / Pearl, L.H. / Wood, S.P. #2: ![]() Title: The Three-Dimensional Structure of Acid Proteinases Authors: Blundell, T.L. / Jenkins, J.A. / Khan, G. / Roychowdhury, P. / Sewell, T. / Tickle, I.J. / Wood, E.A. #3: ![]() Title: Four-Fold Structural Repeat in the Acid Proteases Authors: Blundell, T.L. / Sewell, B.T. / Mclachlan, A.D. #4: ![]() Title: Structural Evidence for Gene Duplication in the Evolution of Acid Proteases Authors: Tang, J. / James, M.N.G. / Hsu, I.N. / Jenkins, J.A. / Blundell, T.L. #5: ![]() Title: Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica Authors: Subramanian, E. / Swan, I.D.A. / Liu, M. / Davies, D.R. / Jenkins, J.A. / Tickle, I.J. / Blundell, T.L. #6: ![]() Title: X-Ray Analysis and Circular Dichroism of the Acid Protease from Endothia Parasitica and Chymosin Authors: Jenkins, J. / Tickle, I. / Sewell, T. / Ungaretti, L. / Wollmer, A. / Blundell, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
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PDB format | ![]() | 56.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.7 KB | Display | ![]() |
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Full document | ![]() | 479.1 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 16.1 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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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUE PRO E 23 AND PRO E 133 ARE CIS PROLINES. 2: THE INHIBITOR RESIDUE CAL I 4 IS CYCLOHEXYL ALA-LEU WITH THE PEPTIDE BOND REPLACED BY CHOH-CH2. |
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Components
#1: Protein | Mass: 33813.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() References: UniProt: P11838, EC: 3.4.23.6 | ||
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#2: Chemical | ChemComp-0EL / ![]() References: 6-ammonio-N-[(2R,4R,5R)-5-{[N-(tert-butoxycarbonyl)-L-phenylalanyl-3-(1H-imidazol-3-ium-4-yl)-L-alanyl]amino}-6- cyclohexyl-4-hydroxy-2-(2-methylpropyl)hexanoyl]-L-norleucylphenylalanine | ||
#3: Water | ChemComp-HOH / | ||
Nonpolymer details | THE INHIBITOR SUBCOMPONESequence details | THE COMPLETE SEQUENCE WAS DETERMINED BY V. PEDERSEN AS TRYPTIC FRAGMENTS WHICH WERE ALIGNED IN THE ...THE COMPLETE SEQUENCE WAS DETERMINED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.32 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.3 / Method: unknownDetails: referred to 'Jenkins, J. A.', (1975) 'J.Mol.Biol.', 99, 583-590 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 0.16 Å / Lowest resolution: 2.1 Å |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→10 Å / Rfactor Rwork: 0.188 Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE ...Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE FOLLOWING RELATION - B = 8 * (PI)**2 * U**2. IT IS AN INDICATION OF POSSIBLE ERRORS IN THE REFINEMENT THAT SOME ARE SLIGHTLY NEGATIVE. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / Rfactor obs: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: o_planar_d / Dev ideal: 0.002 |