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- PDB-3gi5: Crystal structure of protease inhibitor, KB62 in complex with wil... -

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Basic information

Entry
Database: PDB / ID: 3gi5
TitleCrystal structure of protease inhibitor, KB62 in complex with wild type HIV-1 protease
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Drug design / protease inhibitors / HIV-1 protease / Aspartyl protease / Hydrolase / Protease / 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
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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-K62 / PHOSPHATE ION / Protease / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsNalam, M.N.L. / Schiffer, C.A.
CitationJournal: J.Virol. / Year: 2010
Title: Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance.
Authors: Nalam, M.N. / Ali, A. / Altman, M.D. / Reddy, G.S. / Chellappan, S. / Kairys, V. / Ozen, A. / Cao, H. / Gilson, M.K. / Tidor, B. / Rana, T.M. / Schiffer, C.A.
History
DepositionMar 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3784
Polymers21,6322
Non-polymers7472
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-28 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.831, 58.342, 61.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease


Mass: 10815.790 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: SF2 / Gene: pol / Plasmid: PXC35 / Production host: Escherichia Coli (E. coli) / Strain (production host): TAP56 / References: UniProt: O38732, UniProt: P03369*PLUS
#2: Chemical ChemComp-K62 / (5S)-3-(3-Acetylphenyl)-N-[(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-2-hydroxy-1-(phenylmethyl)pr opyl]-2-oxo-5-oxazolidinecarboxamide / (5S)-3-(3-acetylphenyl)-N-{(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-1-benzyl-2-hydroxypropyl}-2- oxo-1,3-oxazolidine-5-carboxamide


Mass: 651.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37N3O9S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.2
Details: 126 mM sodium phosphate pH 6.2, 63 mM sodium citrate, 24-29% ammonium sulphate, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17324 / % possible obs: 98.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.056 / Χ2: 1.092
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.863.50.33914820.944186.1
1.86-1.945.30.26417201199
1.94-2.036.30.2317141.2891100
2.03-2.136.30.18417331.486199.8
2.13-2.276.30.12717331.0861100
2.27-2.446.40.0917451.032199.8
2.44-2.696.40.07117560.986199.9
2.69-3.086.40.05717741.031100
3.08-3.886.30.04317851.034199.9
3.88-506.10.03318820.947199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
AMoREphasing
RefinementResolution: 1.8→25.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.95 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 875 5.1 %RANDOM
Rwork0.17 ---
obs0.171 17282 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 64.56 Å2 / Biso mean: 34.524 Å2 / Biso min: 19.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 51 173 1722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221616
X-RAY DIFFRACTIONr_bond_other_d0.0010.021544
X-RAY DIFFRACTIONr_angle_refined_deg1.3562.0212208
X-RAY DIFFRACTIONr_angle_other_deg0.67733589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.5112556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.90815272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.819158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_nbd_refined0.1740.2227
X-RAY DIFFRACTIONr_nbd_other0.1730.21515
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2752
X-RAY DIFFRACTIONr_nbtor_other0.0790.2971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.218
X-RAY DIFFRACTIONr_mcbond_it0.5021.51068
X-RAY DIFFRACTIONr_mcbond_other0.1011.5420
X-RAY DIFFRACTIONr_mcangle_it0.73121631
X-RAY DIFFRACTIONr_scbond_it0.9973673
X-RAY DIFFRACTIONr_scangle_it1.4684.5577
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 44 -
Rwork0.255 1018 -
all-1062 -
obs--83.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.9232-2.4659-0.70938.48670.44592.2157-0.3503-0.53470.13710.490.32330.070.04160.04520.027-0.10450.0638-0.0047-0.118-0.012-0.294420.792625.669929.1635
24.6653-2.921-0.26014.49851.25485.248-0.1588-0.0424-0.46330.25810.20750.40430.1634-0.0675-0.0488-0.1587-0.00280.0437-0.22180.0332-0.151119.528217.595222.789
33.14680.72340.44613.25990.37291.10130.02290.011-0.03610.0466-0.0341-0.0138-0.02950.01420.0112-0.15040.0042-0.0064-0.14690.002-0.189427.497828.450718.952
44.7958-1.22290.954.68430.13642.09390.1172-0.017-0.1768-0.0162-0.01490.1904-0.06470.0246-0.1023-0.1670.02190.0246-0.17530.0265-0.161512.560126.783118.3493
518.01230.7569-7.2937.89391.67418.2011-0.308-0.5069-0.3565-0.01870.1945-0.65150.2250.50060.1135-0.16010.0095-0.0766-0.1890.0526-0.102238.742230.4724.0359
631.224-13.34670.53156.33211.85546.9261-0.1543-0.4828-1.05610.08530.00340.56530.1143-0.51530.151-0.234-0.0160.0204-0.17550.00550.00661.491621.594817.7172
76.0523-2.0484-1.59287.04084.44927.64470.3161-0.0175-0.0087-0.00850.0627-0.5816-0.32770.4824-0.3787-0.193-0.0083-0.0166-0.15310.0434-0.106939.535431.469610.5877
811.9789-2.3062-1.253210.15242.33113.26210.18130.17550.22650.0939-0.04920.55340.0767-0.4435-0.1321-0.2142-0.00650.0105-0.12050.0997-0.1680.663134.894213.9219
920.57-2.7219-3.39180.6364-0.05322.4147-0.00860.17520.0258-0.0855-0.1011-0.02280.0044-0.06780.1097-0.15530.0067-0.0047-0.1525-0.003-0.189727.427231.06254.557
1015.7364-3.4534-3.93484.0781-1.28352.37210.23480.27310.0661-0.1180.06560.2585-0.1382-0.0222-0.3004-0.15320.0168-0.0063-0.12830.0062-0.148912.806239.433311.589
111.27730.6062-1.24557.2666-2.16613.20770.03520.06080.20080.1566-0.06410.2111-0.2342-0.03330.0289-0.1709-0.0109-0.0182-0.15120.007-0.160429.106433.115714.7288
127.9315-5.63316.302311.0491-7.43286.24810.28730.2163-0.0362-0.2818-0.05020.22650.37690.1052-0.2371-0.14780.026-0.0116-0.14020.017-0.155110.346429.384312.5187
134.46270.07490.74852.1596-0.11232.2312-0.0769-0.0344-0.1226-0.0338-0.0846-0.0405-0.10970.09860.1614-0.14150.01440.0124-0.1559-0.0069-0.11728.828419.815119.4139
141.6841-2.3303-0.88593.7882-0.06413.4173-0.3113-0.3406-0.0986-0.11760.22720.27470.0082-0.07730.0841-0.140.03480.0378-0.10170.0251-0.157511.41328.37726.854
151.1599-2.60310.673913.2478-14.232422.2390.05290.179-0.4179-0.3903-0.7543-0.53040.4450.76540.7013-0.24730.02170.0538-0.11790.0586-0.081839.048323.676710.5499
1610.029411.5967-8.293914.4976-13.830723.37790.5959-0.1580.63540.4620.14880.345-0.4365-0.1853-0.7447-0.22640.09880.0328-0.18070.0201-0.07011.270836.337421.0353
1722.90481.7351-12.63211.5587-1.729219.99210.0309-0.0320.93910.55740.2411-0.2489-0.23240.0574-0.272-0.188-0.0128-0.1021-0.24780.0071-0.084736.938424.441223.8982
1841.0642-31.36063.97239.64023.568115.99890.10911.1319-0.1227-0.09-0.4067-0.16090.74590.46710.2976-0.21710.02280.0659-0.17980.0322-0.12163.039823.121323.6806
192.3092-0.53552.93372.076-1.21188.244-0.13330.08490.01280.039-0.237-0.41460.05430.09080.3703-0.1735-0.00330.003-0.18560.0155-0.127635.794722.166217.3736
201.54772.6004-4.091111.6019-9.024911.45410.0784-0.21080.0119-0.12230.08410.75060.0370.1524-0.1625-0.22250.04370.0173-0.14510.0567-0.06384.024729.460924.686
214.3441-2.6529-3.648812.50017.431913.52330.07750.26460.0669-0.3168-0.06430.1569-0.18480.0845-0.0132-0.0560.0092-0.0067-0.05430.0002-0.110419.169629.754512.7843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION1A6 - 10
4X-RAY DIFFRACTION2B1 - 5
5X-RAY DIFFRACTION2B94 - 99
6X-RAY DIFFRACTION2B6 - 10
7X-RAY DIFFRACTION3A20 - 32
8X-RAY DIFFRACTION4B20 - 32
9X-RAY DIFFRACTION5A11 - 19
10X-RAY DIFFRACTION6B11 - 19
11X-RAY DIFFRACTION7A33 - 43
12X-RAY DIFFRACTION8B33 - 43
13X-RAY DIFFRACTION9A44 - 57
14X-RAY DIFFRACTION10B44 - 57
15X-RAY DIFFRACTION11A77 - 85
16X-RAY DIFFRACTION12B77 - 85
17X-RAY DIFFRACTION13A86 - 93
18X-RAY DIFFRACTION14B86 - 93
19X-RAY DIFFRACTION15A58 - 62
20X-RAY DIFFRACTION16B58 - 62
21X-RAY DIFFRACTION17A63 - 68
22X-RAY DIFFRACTION18B63 - 68
23X-RAY DIFFRACTION19A69 - 76
24X-RAY DIFFRACTION20B69 - 76
25X-RAY DIFFRACTION21A200

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