integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function
1: THERE ARE OXYGENS COVALENTLY BOUND TO SG CYS A 67 AND SG CYS B 67. THEY ARE PRESENTED AS HETATM RECORDS FOLLOWING THE END OF EACH CHAIN.
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Components
#1: Protein
HIV-1PROTEASE
Mass: 10805.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04585
Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details
THE SUBCOMPONENT CAV IN INHIBITOR 1ZK IS THE DIPEPTIDE ISOSTERE CYCLOHEXYL ALANINE PSI(CHOH-CHOH) ...THE SUBCOMPONENT CAV IN INHIBITOR 1ZK IS THE DIPEPTIDE ISOSTERE CYCLOHEXYL ALANINE PSI(CHOH-CHOH)VALINE. THE VALINE HAS A C-OH GROUP IN PLACE OF THE USUAL MAIN CHAIN N ATOM.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
ID
Conc.
Common name
Crystal-ID
Sol-ID
1
20 %(v/v)
ammoniumsulfate
1
reservoir
2
0.1M
sodiumacetate
1
reservoir
3
10mg/ml
proteincomplex
1
drop
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Data collection
Radiation
Scattering type: x-ray
Radiation wavelength
Relative weight: 1
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Processing
Software
Name: PROLSQ / Classification: refinement
Refinement
Rfactor obs: 0.169 / Highest resolution: 2 Å
Refinement step
Cycle: LAST / Highest resolution: 2 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1516
0
59
90
1665
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
p_bond_d
0.02
0.02
X-RAY DIFFRACTION
p_angle_d
0.049
0.035
X-RAY DIFFRACTION
p_angle_deg
X-RAY DIFFRACTION
p_planar_d
0.056
0.05
X-RAY DIFFRACTION
p_hb_or_metal_coord
X-RAY DIFFRACTION
p_mcbond_it
1.475
1.5
X-RAY DIFFRACTION
p_mcangle_it
2.21
2
X-RAY DIFFRACTION
p_scbond_it
4.215
3
X-RAY DIFFRACTION
p_scangle_it
5.934
4
X-RAY DIFFRACTION
p_plane_restr
0.017
0.02
X-RAY DIFFRACTION
p_chiral_restr
0.201
0.15
X-RAY DIFFRACTION
p_singtor_nbd
0.191
0.3
X-RAY DIFFRACTION
p_multtor_nbd
0.201
0.3
X-RAY DIFFRACTION
p_xhyhbond_nbd
0.185
0.3
X-RAY DIFFRACTION
p_xyhbond_nbd
X-RAY DIFFRACTION
p_planar_tor
2.8
3
X-RAY DIFFRACTION
p_staggered_tor
17.6
10
X-RAY DIFFRACTION
p_orthonormal_tor
17.2
20
X-RAY DIFFRACTION
p_transverse_tor
X-RAY DIFFRACTION
p_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 10110 / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
+
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