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- PDB-3ekp: Crystal Structure of the inhibitor Amprenavir (APV) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3ekp
TitleCrystal Structure of the inhibitor Amprenavir (APV) in complex with a multi-drug resistant HIV-1 protease variant (L10I/G48V/I54V/V64I/V82A)Refer: FLAP+ in citation
ComponentsProtease
KeywordsHYDROLASE / HIV-1 / protease / multi-drug resistance / Amprenavir / AIDS
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / 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 / symbiont entry into host cell / viral translational frameshifting / 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. / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / 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
Chem-478 / ACETATE ION / PHOSPHATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsPrabu-Jayabalan, M. / King, N.M. / Bandaranayake, R.M.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease.
Authors: King, N.M. / Prabu-Jeyabalan, M. / Bandaranayake, R.M. / Nalam, M.N. / Nalivaika, E.A. / Ozen, A. / Yilmaz, N.K. / Schiffer, C.A.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Oct 17, 2012Group: Database references
Revision 1.4Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 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
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,36322
Polymers43,2634
Non-polymers2,10018
Water4,720262
1
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,87113
Polymers21,6322
Non-polymers1,24011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-54 kcal/mol
Surface area9240 Å2
MethodPISA
2
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4919
Polymers21,6322
Non-polymers8607
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-24 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.969, 91.969, 106.222
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Protease / Retropepsin / PR


Mass: 10815.788 Da / Num. of mol.: 4 / Fragment: UNP residues 491-589 / Mutation: Q7K,L10I,G48V,I54V,V64I,V82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-478 / {3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER / Amprenavir


Mass: 505.627 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H35N3O6S / Comment: protease inhibitor, medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Refer citation, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→23.75 Å / Num. all: 27531 / Num. obs: 27531 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→23.75 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0 / SU B: 8.159 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1384 5 %RANDOM
Rwork0.196 ---
all0.199 27472 --
obs0.199 27472 99.33 %-
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: 81.08 Å2 / Biso mean: 39.665 Å2 / Biso min: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.15→23.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 138 262 3360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223214
X-RAY DIFFRACTIONr_bond_other_d0.0010.023109
X-RAY DIFFRACTIONr_angle_refined_deg1.3312.0144388
X-RAY DIFFRACTIONr_angle_other_deg0.66237191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.275410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7424.766107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.215501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4371516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023542
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02584
X-RAY DIFFRACTIONr_nbd_refined0.1950.2517
X-RAY DIFFRACTIONr_nbd_other0.2010.23279
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21472
X-RAY DIFFRACTIONr_nbtor_other0.0880.22129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.211
X-RAY DIFFRACTIONr_mcbond_it1.2081.52631
X-RAY DIFFRACTIONr_mcbond_other0.2451.5846
X-RAY DIFFRACTIONr_mcangle_it1.4223300
X-RAY DIFFRACTIONr_scbond_it2.28831299
X-RAY DIFFRACTIONr_scangle_it3.3244.51088
LS refinement shellResolution: 2.15→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 98 -
Rwork0.222 1921 -
all-2019 -
obs--100 %
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)
13.62630.42743.21873.09231.80216.61340.04650.057-0.24990.00330.0554-0.09220.15310.1265-0.1019-0.07180.00040.0041-0.05070-0.049820.9981-36.360935.3864
28.24935.6706-4.627813.4739-1.91952.7623-0.17910.5362-0.16850.28140.2099-0.10510.0467-0.6468-0.0308-0.0777-0.0220.01450.09970.02340.014412.7008-26.961930.8242
314.53260.5525-4.04953.9803-2.81622.91850.28170.21460.33820.355-0.00860.5013-0.31350.7033-0.27310.0242-0.10150.0038-0.0389-0.0036-0.01916.9998-24.432539.9866
46.7381.66157.88780.7444-1.88453.038-0.065-0.31150.17090.54690.1674-0.10630.1452-1.3558-0.1023-0.10260.0573-0.0277-0.0566-0.0176-0.05545.2153-16.59730.3244
53.8832.70795.1272.3444-0.066435.85380.14950.3480.0626-0.3626-0.08150.1928-0.62510.8106-0.068-0.03320.0079-0.0134-0.1179-0.028-0.021512.0161-13.0340.9781
615.6093-8.83088.11127.0054-9.438415.91920.22660.6364-0.43880.0348-0.03230.18110.0713-0.3976-0.1943-0.1088-0.0916-0.0081-0.0392-0.0184-0.09819.0083-26.417116.5254
72.907-5.1776-5.076217.27715.65513.04910.15030.02520.00570.36280.0951-0.5963-0.36430.4014-0.2455-0.1693-0.06330.005-0.01350.0311-0.096113.341-29.656154.2918
88.10724.8514-6.800911.0201-1.26536.674-0.01490.4432-0.5281-0.85860.41330.12251.07820.6501-0.3984-0.0843-0.07530.0808-0.0811-0.0613-0.073322.9968-31.80517.3042
99.222-6.3396-3.4598.3591-0.45773.30690.3799-0.8967-0.2831.03810.0114-0.76320.83670.4313-0.3912-0.104-0.0464-0.05930.040.0791-0.075915.9663-35.383454.1
1010.6468-3.191-0.9313.284-1.75691.86220.2287-0.26481.34850.3411-0.198-0.6135-0.3893-0.5932-0.0307-0.02740.01420.01940.02650.08610.081614.8865-18.108725.2031
110.90031.0709-1.36299.89192.59264.12370.08550.75370.4440.0706-0.06391.3095-0.53040.1951-0.0216-0.0539-0.02240.1017-0.0666-0.00280.0768.2425-21.948645.6235
124.4727-0.9717-1.31831.20481.90323.01910.01090.3908-0.0964-0.4990.0715-0.02690.0621-0.6076-0.0824-0.0253-0.05260.00180.04590.0007-0.014214.9308-31.530725.5487
130.90710.18190.94521.4223-1.88474.0894-0.0092-0.44180.20870.4321-0.1344-0.0661-0.37270.30850.1436-0.0055-0.05150.00160.03020.02740.00119.8502-28.697745.246
142.36323.32350.15965.8021-1.04231.43310.0746-0.11930.2557-0.11230.04290.4341-0.2994-0.538-0.1176-0.06820.05830.0093-0.016-0.0004-0.00164.077550.7538-8.8579
1510.6665-0.51791.8350.0371-0.38027.41940.1369-0.1421-0.0612-0.6059-0.03070.50220.24090.3429-0.10620.01630.0238-0.0195-0.01930.0126-0.022312.220340.1592-7.8884
165.2711-6.2254-2.63457.35623.24656.09530.1251-0.29620.28060.03950.03870.07020.35250.3496-0.1638-0.02430.0060.02220.0228-0.0011-0.027417.313848.9827-9.8285
175.53365.2034-6.262711.1771-10.41110.9250.4685-0.2922-0.0381-0.2193-0.7817-0.09460.32420.31640.3133-0.01860.0817-0.09-0.0015-0.054-0.043922.257832.5055-8.6074
183.95522.8761-6.01016.8109-8.148712.15750.0292-0.5334-0.0594-0.6541-0.1868-0.1318-0.05790.27120.1576-0.06850.0533-0.04160.0179-0.1176-0.000728.963544.1672-9.1136
191.3674-5.72561.295140.23243.24079.9965-0.0745-0.0775-0.12041.1289-0.23750.73330.6666-0.58570.312-0.1479-0.0877-0.03750.00380.0146-0.06996.297835.42835.7032
2062.681220.94947.483712.74132.63864.2739-0.6722-0.01120.46-0.64020.19260.2074-0.70450.18190.47960.0520.03950.0604-0.2234-0.0731-0.149518.351556.4136-23.395
2111.49322.0323-6.5010.3593-1.14953.67730.79660.010.1258-0.2139-1.36591.77630.116-1.52180.5693-0.0639-0.0906-0.07910.2306-0.0416-0.07581.469439.92925.1474
2226.82914.23742.74817.7937-5.85186.6278-0.69320.9920.5184-0.95190.63580.5105-0.66060.10130.05730.160.10120.006-0.1018-0.0515-0.097311.95558.5295-23.5768
232.00812.47450.72154.20831.33752.32920.12170.2202-0.06490.09340.1866-0.22480.30690.3439-0.3083-0.025-0.0233-0.0421-0.01550.0132-0.012417.939536.58410.3617
240.94551.73340.69854.041-0.45714.01290.20390.0654-0.05580.17890.1747-0.1280.00470.4501-0.3786-0.025-0.01190.0257-0.029-0.05030.003323.298245.8608-18.0685
257.50061.4307-5.35350.3045-0.89734.30570.4123-0.3703-0.39440.0767-0.15350.08130.1287-0.1482-0.2588-0.0611-0.0305-0.0256-0.00860.0042-0.00645.926838.9595-4.4965
266.6554-4.40772.82847.649-5.74484.37120.0970.03250.1399-0.60560.2129-0.1152-0.6860.1496-0.30990.0364-0.0019-0.0006-0.0685-0.0205-0.000115.211555.0308-13.1973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION1B1 - 5
4X-RAY DIFFRACTION1B94 - 99
5X-RAY DIFFRACTION2A25 - 30
6X-RAY DIFFRACTION3B25 - 30
7X-RAY DIFFRACTION4A45 - 55
8X-RAY DIFFRACTION5B45 - 55
9X-RAY DIFFRACTION6A60 - 66
10X-RAY DIFFRACTION7B60 - 66
11X-RAY DIFFRACTION8A68 - 72
12X-RAY DIFFRACTION9B68 - 72
13X-RAY DIFFRACTION10A74 - 84
14X-RAY DIFFRACTION11B74 - 84
15X-RAY DIFFRACTION12A86 - 92
16X-RAY DIFFRACTION13B86 - 92
17X-RAY DIFFRACTION14C1 - 5
18X-RAY DIFFRACTION14C94 - 99
19X-RAY DIFFRACTION14D1 - 5
20X-RAY DIFFRACTION14D94 - 99
21X-RAY DIFFRACTION15C25 - 30
22X-RAY DIFFRACTION16D25 - 30
23X-RAY DIFFRACTION17C45 - 55
24X-RAY DIFFRACTION18D45 - 55
25X-RAY DIFFRACTION19C60 - 66
26X-RAY DIFFRACTION20D60 - 66
27X-RAY DIFFRACTION21C68 - 72
28X-RAY DIFFRACTION22D68 - 72
29X-RAY DIFFRACTION23C74 - 84
30X-RAY DIFFRACTION24D74 - 84
31X-RAY DIFFRACTION25C86 - 92
32X-RAY DIFFRACTION26D86 - 92

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