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- PDB-3gi4: Crystal structure of protease inhibitor, KB60 in complex with wil... -

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Basic information

Entry
Database: PDB / ID: 3gi4
TitleCrystal structure of protease inhibitor, KB60 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


RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / 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. / 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 / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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
ACETATE ION / Chem-K60 / PHOSPHATE ION / Protease / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 1.85 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

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6177
Polymers21,6322
Non-polymers9865
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-33 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.809, 58.131, 61.568
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-K60 / 5S)-N-[(1S,2R)-3-[(1,3-Benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-2-hydroxy-1-(phenylmethyl)propyl]-2-oxo-3-[3-(tr ifluoromethyl)phenyl]-5-oxazolidinecarboxamide / (5S)-N-{(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-1-benzyl-2-hydroxypropyl}-2-oxo-3-[3-(trifluoro methyl)phenyl]-1,3-oxazolidine-5-carboxamide


Mass: 677.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H34F3N3O8S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
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: 1.85→50 Å / Num. obs: 16121 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.06 / Χ2: 1.006
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.924.70.31915470.92197.4
1.92-1.996.60.27215780.9851100
1.99-2.086.80.23115891.2151100
2.08-2.196.90.1715951.0171100
2.19-2.336.90.12115890.9511100
2.33-2.516.90.09315990.9831100
2.51-2.7670.07216211.0231100
2.76-3.1670.05216171.0061100
3.16-3.996.90.03516411.0121100
3.99-506.60.02617450.926199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
AMoREphasing
RefinementResolution: 1.85→25.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.572 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 808 5 %RANDOM
Rwork0.169 ---
obs0.172 16079 99.57 %-
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: 61.8 Å2 / Biso mean: 24.766 Å2 / Biso min: 10.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 65 139 1690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221620
X-RAY DIFFRACTIONr_bond_other_d0.0010.021538
X-RAY DIFFRACTIONr_angle_refined_deg1.4032.0262217
X-RAY DIFFRACTIONr_angle_other_deg0.69833562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.74824.73757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.14115262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.18159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02292
X-RAY DIFFRACTIONr_nbd_refined0.1750.2234
X-RAY DIFFRACTIONr_nbd_other0.180.21512
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2753
X-RAY DIFFRACTIONr_nbtor_other0.0790.2953
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.090.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1670.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.27
X-RAY DIFFRACTIONr_mcbond_it0.5271.51070
X-RAY DIFFRACTIONr_mcbond_other0.1091.5420
X-RAY DIFFRACTIONr_mcangle_it0.74721632
X-RAY DIFFRACTIONr_scbond_it0.9973663
X-RAY DIFFRACTIONr_scangle_it1.524.5585
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 55 -
Rwork0.207 1061 -
all-1116 -
obs--94.9 %
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)
13.7483-2.1511-1.1897.51290.943.3992-0.3049-0.37150.07110.38890.27080.0977-0.05390.07290.0341-0.04530.05360.006-0.0474-0.0005-0.162720.88925.648929.1693
24.4168-2.40951.08314.39511.23535.2675-0.1551-0.0689-0.46460.21480.20690.37860.1904-0.0312-0.0518-0.0598-0.00120.0501-0.14470.0398-0.063519.575517.56222.8858
33.18070.77560.33033.427-0.14430.673-0.0294-0.03240.06670.0062-0.07980.0213-0.0683-0.00430.1092-0.0453-0.0016-0.0063-0.0587-0.0001-0.098927.519128.360718.9586
45.8594-0.91280.96881.8017-0.21642.72210.0276-0.0485-0.16480.01790.05950.15750.0095-0.0455-0.0871-0.07530.01610.0186-0.10410.016-0.058713.17726.877618.7501
513.40140.5537-1.70079.54311.86755.1157-0.0813-0.4423-0.22520.0863-0.116-0.7997-0.02710.41410.1972-0.0529-0.0074-0.0786-0.10830.0657-0.037238.827430.445524.0325
637.2034-13.6864-2.0467.00611.19965.54630.00060.0691-1.08380.1088-0.07870.5182-0.0613-0.46690.0781-0.1009-0.01340.0109-0.0808-0.00080.0481.521.513617.8042
76.2016-0.9871-0.60285.03273.55276.66910.26580.0196-0.0679-0.0094-0.0175-0.5579-0.33850.391-0.2483-0.0756-0.0202-0.0199-0.08070.0393-0.026339.531431.341210.5904
89.3919-3.4156-1.695310.84092.68362.67960.20930.19990.29740.0512-0.04950.31690.0329-0.4403-0.1598-0.1038-0.00330.0099-0.01630.0872-0.05710.641534.858113.8977
913.8593-1.9997-3.93491.66210.09423.0268-0.04290.2503-0.0751-0.1058-0.056-0.0003-0.0692-0.06870.099-0.05350.0179-0.0056-0.0824-0.009-0.089827.317431.22494.5574
1015.6581-4.1343-1.62613.1061-1.52792.07050.15150.1566-0.1903-0.01120.01420.2655-0.05880.0698-0.1657-0.0407-0.0089-0.0041-0.06530.0034-0.05412.990239.108311.6885
111.35941.7126-1.59015.4525-1.03115.26250.00350.11190.12880.1128-0.06180.1943-0.4086-0.10930.0583-0.056-0.0106-0.0229-0.05990.008-0.076829.131933.003614.7109
125.5011-5.9386.934910.533-7.62038.74690.27630.2253-0.1121-0.3682-0.08610.27670.40020.4167-0.1902-0.06060.0059-0.0197-0.05080.0173-0.035910.337329.280912.5541
132.8877-0.69660.15472.752-1.76441.1627-0.01420.0346-0.15970.0376-0.098-0.0218-0.04120.16160.1122-0.04220.00360.0081-0.0641-0.0135-0.02628.845219.724819.4863
144.6275-2.1295-3.53355.8687-0.00374.497-0.3017-0.3374-0.0819-0.04910.36120.31330.0356-0.045-0.0595-0.06480.04660.0237-0.01720.0264-0.068311.469428.371326.8952
151.8343-2.78886.672913.9644-15.838929.32290.22850.1965-0.7251-0.6194-0.6111-0.58720.59720.64570.3826-0.16720.02850.0753-0.01970.0662-0.008239.05823.539210.5652
1613.06910.093-10.480615.4309-14.846822.09070.6058-0.14540.67750.59260.06210.6408-0.57360.1262-0.6679-0.12550.07750.0224-0.0970.02810.01461.280536.276421.0234
1725.53022.9074-17.07211.6663-4.330731.30510.0607-0.22751.14090.46960.099-0.1023-0.3037-0.0996-0.1597-0.1229-0.0404-0.0994-0.16990.00370.015636.983524.362223.9367
1828.8247-17.15278.068614.7409-0.399814.6849-0.03770.86840.1984-0.0418-0.4347-0.54930.78090.41290.4724-0.1080.0220.0726-0.07420.0776-0.00663.073423.194223.7467
190.3883-0.4781.87642.3949-1.12099.851-0.10980.0795-0.07680.0179-0.0754-0.30670.03650.10590.1851-0.1001-0.00580.0134-0.06550.03-0.03435.808122.041817.41
202.26892.3547-4.29977.7736-6.64049.861-0.1431-0.17330.0236-0.17090.09430.22760.1615-0.04580.0488-0.10010.03980.0136-0.07420.0306-0.01524.060729.39824.7078
216.4898-1.24-3.02237.91016.302611.74430.16130.2870.0855-0.26860.08680.0554-0.21030.084-0.2482-0.08030.0137-0.0036-0.07250.0175-0.120119.195629.797413.0472
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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