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- PDB-3hvp: CONSERVED FOLDING IN RETROVIRAL PROTEASES. CRYSTAL STRUCTURE OF A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hvp | ||||||
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Title | CONSERVED FOLDING IN RETROVIRAL PROTEASES. CRYSTAL STRUCTURE OF A SYNTHETIC HIV-1 PROTEASE | ||||||
![]() | UNLIGANDED HIV-1 PROTEASE | ||||||
![]() | HYDROLASE(ACID PROTEINASE) | ||||||
Function / homology | ![]() HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Wlodawer, A. / Jaskolski, M. / Miller, M. | ||||||
![]() | ![]() Title: Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Authors: Wlodawer, A. / Miller, M. / Jaskolski, M. / Sathyanarayana, B.K. / Baldwin, E. / Weber, I.T. / Selk, L.M. / Clawson, L. / Schneider, J. / Kent, S.B. #1: ![]() Title: Molecular Modeling of the HIV-1 Protease and its Substrate Binding Site Authors: Weber, I.T. / Miller, M. / Jaskolski, M. / Leis, J. / Skalka, A.M. / Wlodawer, A. #2: ![]() Title: Crystal Structure of a Retroviral Protease Proves Relationship to Aspartic Protease Family Authors: Miller, M. / Jaskolski, M. / Rao, J.K.M. / Leis, J. / Wlodawer, A. #3: ![]() Title: Enzymatic Activity of a Synthetic 99 Residue Protein Corresponding to the Putative HIV-1 Protease Authors: Schneider, J. / Kent, S.B.H. | ||||||
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. INT 4 PRO 1 THR 4 0 INT 4 THR 96 PHE 99 -1 INT 4 THR 96 PHE 99 -1 INT 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 | ![]() | 28.4 KB | Display | ![]() |
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PDB format | ![]() | 21.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 368.4 KB | Display | ![]() |
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Full document | ![]() | 383.6 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.7 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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1 | ![]()
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Unit cell |
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Details | THE ACTIVE ENZYME IS FORMED BY TWO CRYSTALLOGRAPHICALLY RELATED MOLECULES. TO GENERATE THE OTHER MOLECULE ONE MUST APPLY THE CRYSTALLOGRAPHIC TWO-FOLD (Y, X, -Z) TO THE COORDINATES IN THIS ENTRY. |
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Components
#1: Protein | Mass: 10764.636 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.59 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.8 Å / Num. all: 26037 / Num. obs: 3225 / Rmerge(I) obs: 1.5 |
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Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.184 / Highest resolution: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Rfactor obs: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.9 Å2 |