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Yorodumi- PDB-4hvp: Structure of complex of synthetic HIV-1 protease with a substrate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hvp | ||||||
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Title | Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 Angstroms resolution | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Miller, M. / Schneider, J. / Sathyanarayana, B.K. / Toth, M.V. / Marshall, G.R. / Clawson, L. / Selk, L. / Kent, S.B.H. / Wlodawer, A. | ||||||
Citation | Journal: Science / Year: 1989 Title: Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. Authors: Miller, M. / Schneider, J. / Sathyanarayana, B.K. / Toth, M.V. / Marshall, G.R. / Clawson, L. / Selk, L. / Kent, S.B. / Wlodawer, A. #1: Journal: Science / Year: 1989 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.H. #2: Journal: Science / Year: 1989 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. #3: Journal: Nature / Year: 1989 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. #4: Journal: Cell(Cambridge,Mass.) / Year: 1988 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 | THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING A ...THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING A FOUR-STRANDED ANTIPARALLEL BETA-SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hvp.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hvp.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 4hvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hvp_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 4hvp_full_validation.pdf.gz | 481.9 KB | Display | |
Data in XML | 4hvp_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 4hvp_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/4hvp ftp://data.pdbj.org/pub/pdb/validation_reports/hv/4hvp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: THE PEPTIDE BOND BETWEEN RESIDUES NLE I 3 AND NLE I 4 HAS BEEN REDUCED AND IS -CH2-NH-. |
-Components
#1: Protein | Mass: 10764.636 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03369 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THE PEPTIDE BOND BETWEEN SUBCOMPONE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.57 % | |||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 5.4 | |||||||||||||||
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: 2.25 Å / Num. all: 8740 / Num. obs: 7943 / Observed criterion σ(I): 1.5 / Num. measured all: 55569 / Rmerge(I) obs: 0.068 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→10 Å /
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: 'X-PLOR, PROLSQ' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.176 / Highest resolution: 2.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |