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- PDB-7doz: HIV-1 Protease D30N mutant in complex with Nelfinavir -

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Basic information

Entry
Database: PDB / ID: 7doz
TitleHIV-1 Protease D30N mutant in complex with Nelfinavir
ComponentsProtease
KeywordsVIRAL PROTEIN / HIV Protease
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-1UN / Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsBihani, S.C. / Hosur, M.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2021
Title: Molecular basis for reduced cleavage activity and drug resistance in D30N HIV-1 protease.
Authors: Bihani, S.C. / Gupta, G.D. / Hosur, M.V.
History
DepositionDec 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0683
Polymers21,9331
Non-polymers1,1362
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-10 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.050, 62.050, 81.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Protease / Retropepsin


Mass: 21932.789 Da / Num. of mol.: 1 / Mutation: D30N,C95M,C1095A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q72874
#2: Chemical ChemComp-1UN / 2-[2-HYDROXY-3-(3-HYDROXY-2-METHYL-BENZOYLAMINO)-4-PHENYL SULFANYL-BUTYL]-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID TERT-BUTYLAMIDE / NELFINAVIR MESYLATE AG1343


Mass: 567.782 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H45N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 2% saturated Ammonium Sulfate, 200/100 mM phosphate citrate buffer,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979778 Å / Relative weight: 1
ReflectionResolution: 1.91→26.87 Å / Num. obs: 13778 / % possible obs: 99.5 % / Redundancy: 4.27 % / Biso Wilson estimate: 23.35 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.46
Reflection shellResolution: 1.91→2.01 Å / Rmerge(I) obs: 0.51 / Num. unique obs: 1951

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kt2

3kt2


Resolution: 1.91→26.87 Å / SU ML: 0.2365 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 23.7884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228 688 5 %
Rwork0.1825 13082 -
obs0.1848 13770 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.75 Å2
Refinement stepCycle: LAST / Resolution: 1.91→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 80 146 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641628
X-RAY DIFFRACTIONf_angle_d0.97642211
X-RAY DIFFRACTIONf_chiral_restr0.0592260
X-RAY DIFFRACTIONf_plane_restr0.0064269
X-RAY DIFFRACTIONf_dihedral_angle_d17.9475598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-2.060.28531370.23042601X-RAY DIFFRACTION99.42
2.06-2.260.26331370.2022608X-RAY DIFFRACTION99.71
2.26-2.590.2391380.19972625X-RAY DIFFRACTION99.93
2.59-3.260.27431390.19362635X-RAY DIFFRACTION99.93
3.27-26.870.17841370.15542613X-RAY DIFFRACTION98.43
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)
16.01349257791.153999137443.063912180432.182750042830.8631794043094.105848609040.07150525412180.443918225357-0.262037175013-0.2025079280640.04138336202280.1056480234870.1271062039370.384736843328-0.03868965965130.1539901999-0.027144063579-0.01884682456230.189865015175-0.0234897991560.163559581988-17.115943125516.37878884119.1261823598
23.724964469362.468559150441.952012858933.527484737942.78993680823.955957822580.172663033858-0.21243545245-0.1535402384520.44979460824-0.0111961581225-0.3644415457750.406168596222-0.0654993912172-0.0597909909850.174667426792-0.0332123185761-0.04609387543320.1732808957430.007184712420750.199917445766-5.6522872395123.041572662536.4786040522
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 99 )1 - 991 - 99
22chain 'A' and (resid 1001 through 1099 )1001 - 1099100 - 198

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