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- PDB-2fxd: X-ray crystal structure of HIV-1 protease IRM mutant complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2fxd
TitleX-ray crystal structure of HIV-1 protease IRM mutant complexed with atazanavir (BMS-232632)
Componentspol protein
KeywordsHYDROLASE / HUMAN IMMUNODEFICIENCY VIRUS (HIV) / HIV-1 PROTEASE / REYATAZ / ATAZANAVIR / BMS-232632
Function / homology
Function and homology information


viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function
Reverse transcriptase thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) ...Reverse transcriptase thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Chem-DR7 / : / Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.6 Å
AuthorsKlei, H.E. / Sheriff, S.
CitationJournal: J.Virol. / Year: 2007
Title: X-ray crystal structures of human immunodeficiency virus type 1 protease mutants complexed with atazanavir.
Authors: Klei, H.E. / Kish, K. / Lin, P.F. / Guo, Q. / Friborg, J. / Rose, R.E. / Zhang, Y. / Goldfarb, V. / Langley, D.R. / Wittekind, M. / Sheriff, S.
History
DepositionFeb 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pol protein
B: pol protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3795
Polymers21,5192
Non-polymers8603
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-42 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.381, 58.214, 61.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein pol protein


Mass: 10759.678 Da / Num. of mol.: 2 / Fragment: HIV-1 PROTEASE
Mutation: Q7K,L10I,I13V,L33I,S37N,R41K,M46I,L63I,C67A,V82F,I84V,L90M,C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 21929323, UniProt: Q90HG9*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-DR7 / (3S,8S,9S,12S)-3,12-BIS(1,1-DIMETHYLETHYL)-8-HYDROXY-4,11-DIOXO-9-(PHENYLMETHYL)-6-[[4-(2-PYRIDINYL)PHENYL]METHYL]-2,5, 6,10,13-PENTAAZATETRADECANEDIOIC ACID DIMETHYL ESTER / ATAZANAVIR / METHYL [(1S,4S,5S,10S)-4-BENZYL-1,10-DI-TERT-BUTYL-5-HYDROXY-2,9,12-TRIOXO-7-(4-PYRIDIN-2-YLBENZYL)-13-OXA-3,7,8,11-TETRAAZATET RADEC-1-YL]CARBAMATE


Mass: 704.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H52N6O7 / Comment: medication, antiretroviral*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 145 mM disodium monohydrogen phosphate, 27 mM sodium citrate monohydrate, 30% saturated ammonium sulfate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: BRUKER / Detector: CCD / Date: Jun 19, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.6→20 Å / Num. all: 25198 / Num. obs: 25198 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.7 / % possible all: 87.5

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Processing

Software
NameVersionClassification
HKL-2000(DENZO)data collection
HKL-2000(SCALEPACK)data reduction
AMoREphasing
CNX2005refinement
HKL-2000(SCALEPACK)data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 2FXE

2fxe


Resolution: 1.6→19.67 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 956627.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 974 3.9 %RANDOM
Rwork0.235 ---
all0.235 ---
obs0.235 25196 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.5141 Å2 / ksol: 0.460799 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---4.28 Å20 Å2
3---4.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 60 193 1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shellResolution: 1.6→1.67 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.365 132 4.7 %
Rwork0.367 2691 -
obs--89.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramwater.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5ligand.paramligand.top

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