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- PDB-3hvp: CONSERVED FOLDING IN RETROVIRAL PROTEASES. CRYSTAL STRUCTURE OF A... -

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Basic information

Entry
Database: PDB / ID: 3hvp
TitleCONSERVED FOLDING IN RETROVIRAL PROTEASES. CRYSTAL STRUCTURE OF A SYNTHETIC HIV-1 PROTEASE
ComponentsUNLIGANDED HIV-1 PROTEASE
KeywordsHYDROLASE(ACID PROTEINASE)
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsWlodawer, A. / Jaskolski, M. / Miller, M.
Citation
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.
#1: 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.
#2: 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.
#3: 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
DepositionAug 8, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 700SHEET 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 viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UNLIGANDED HIV-1 PROTEASE


Theoretical massNumber of molelcules
Total (without water)10,7651
Polymers10,7651
Non-polymers00
Water00
1
A: UNLIGANDED HIV-1 PROTEASE

A: UNLIGANDED HIV-1 PROTEASE


Theoretical massNumber of molelcules
Total (without water)21,5292
Polymers21,5292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3220 Å2
ΔGint-16 kcal/mol
Surface area10120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.240, 50.240, 106.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE 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 UNLIGANDED HIV-1 PROTEASE


Mass: 10764.636 Da / Num. of mol.: 1
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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.59 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112.5 %(w/v)PEG140001drop
210-30 %ammonium sulfate1reservoir
3protein1drop1mg

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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

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.184 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 0 0 758
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.021
X-RAY DIFFRACTIONp_angle_d0.0760.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0970.058
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3361
X-RAY DIFFRACTIONp_mcangle_it2.3151.5
X-RAY DIFFRACTIONp_scbond_it3.7952.5
X-RAY DIFFRACTIONp_scangle_it5.4743
X-RAY DIFFRACTIONp_plane_restr0.0250.024
X-RAY DIFFRACTIONp_chiral_restr0.2640.16
X-RAY DIFFRACTIONp_singtor_nbd0.2710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2970.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2040.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.43.9
X-RAY DIFFRACTIONp_staggered_tor19.410
X-RAY DIFFRACTIONp_orthonormal_tor28.140
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.9 Å2

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