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- PDB-2sam: STRUCTURE OF THE PROTEASE FROM SIMIAN IMMUNODEFICIENCY VIRUS: COM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2sam | ||||||
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Title | STRUCTURE OF THE PROTEASE FROM SIMIAN IMMUNODEFICIENCY VIRUS: COMPLEX WITH AN IRREVERSIBLE NON-PEPTIDE INHIBITOR | ||||||
![]() | SIV PROTEASE | ||||||
![]() | HYDROLASE(ACID PROTEASE) | ||||||
Function / homology | ![]() exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Rose, R.B. / Rose, J.R. / Salto, R. / Craik, C.S. / Stroud, R.M. | ||||||
![]() | ![]() Title: Structure of the protease from simian immunodeficiency virus: complex with an irreversible nonpeptide inhibitor. Authors: Rose, R.B. / Rose, J.R. / Salto, R. / Craik, C.S. / Stroud, R.M. | ||||||
History |
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Remark 700 | SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING ...SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING A FOUR-STRANDED ANTIPARALLEL BETA-SHEET. BECAUSE OF LIMITATIONS IMPOSED BY THE PROTEIN DATA BANK FORMAT IT IS NOT POSSIBLE TO PRESENT THIS SHEET ON SHEET RECORDS. INSTEAD THIS SHEET IS SPECIFIED IN THIS REMARK. STRANDS 1 AND 3 ARE FROM THE MOLECULE IN THIS ENTRY AND STRANDS 2 AND 4 ARE FROM THE SYMMETRY RELATED MOLECULE. I 4 PRO 1 THR 4 0 I 4 THR 96 PHE 99 -1 I 4 THR 96 PHE 99 -1 I 4 PRO 1 THR 4 -1 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29.3 KB | Display | ![]() |
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PDB format | ![]() | 21.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar 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: THE EPN INHIBITOR IS COVALENTLY BOUND TO OD2 OF ASP 25. | ||||||||
Components on special symmetry positions |
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Details | THE HIV-1 PROTEASE IS A DIMER. IN THE CRYSTAL THE TWO MONOMERS ARE RELATED BY A CRYSTALLOGRAPHIC TWO-FOLD AXIS. TO GENERATE THE SYMMETRY RELATED MONOMER, THE FOLLOWING TRANSFORMATION MUST BE APPLIED TO THE COORDINATES PRESENTED IN THIS ENTRY MTRIX1 1 1.000000 0.000000 0.000000 0.000000 MTRIX2 1 0.000000 -1.000000 0.000000 0.000000 MTRIX3 1 0.000000 0.000000 -1.000000 0.000000 |
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Components
#1: Protein | Mass: 10782.454 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Chemical | ChemComp-EPN / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE OCCUPANCY OF THE LIGAND, EPNP, WAS REFINED TO 0.5. THE STOICHIOMETRY OF BINDING OF EPNP TO SIV ...THE OCCUPANCY OF THE LIGAND, EPNP, WAS REFINED TO 0.5. THE STOICHIOME |
Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: POL_ ...SEQUENCE ADVISORY NOTICE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.28 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop / Details: using macroseeding | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 8824 / % possible obs: 92 % / Observed criterion σ(I): 1 / Num. measured all: 21880 / Rmerge(I) obs: 0.054 |
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Reflection shell | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 2.5 Å / % possible obs: 77 % |
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Processing
Software |
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Refinement | Resolution: 2.4→40 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.2 |