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- PDB-2fnt: Crystal structure of a drug-resistant (V82A) inactive (D25N) HIV-... -

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Basic information

Entry
Database: PDB / ID: 2fnt
TitleCrystal structure of a drug-resistant (V82A) inactive (D25N) HIV-1 protease complexed with AP2V variant of HIV-1 NC-p1 substrate.
Components
  • NC-p1 substrate PEPTIDE
  • protease
KeywordsHYDROLASE / structural intermediate / substrate recognition / hiv-1 protease / NC-p1 substrate / drug resistance / flap conformation
Function / homology
Function and homology information


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 ...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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / 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 / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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 / PHOSPHATE ION / Protease / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsPrabu-Jeyabaln, M. / Nalivaika, E.A. / Schiffer, C.A.
Citation
Journal: J.Virol. / Year: 2006
Title: Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate.
Authors: Prabu-Jeyabalan, M. / Nalivaika, E.A. / Romano, K. / Schiffer, C.A.
#1: Journal: J.Virol. / Year: 2004
Title: Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease.
Authors: Prabu-Jeyabaln, M. / Nalivaika, E.A. / King, N.M. / Schiffer, C.A.
History
DepositionJan 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 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 1.5Aug 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

Downloads & links

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Assembly

Deposited unit
A: protease
B: protease
P: NC-p1 substrate PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,48312
Polymers22,7363
Non-polymers7479
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-60 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.056, 57.623, 61.475
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 protease / / Retropepsin / PR


Mass: 10772.724 Da / Num. of mol.: 2 / Mutation: Q7K, D25N, L63P, I64V, V82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: HXB2 / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106
References: UniProt: O38716, UniProt: P03369*PLUS, HIV-1 retropepsin
#2: Protein/peptide NC-p1 substrate PEPTIDE


Mass: 1190.395 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in drug-resistant HIV
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Sodium phosphate pH 6.2; 63mM sodium citrate; ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jun 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. all: 33155 / Num. obs: 33155 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 10.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T3R

1t3r


Resolution: 1.44→41.88 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.404 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 1662 5 %RANDOM
Rwork0.18698 ---
all0.18829 33155 --
obs0.18829 31723 99.58 %-
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 mean: 17.784 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---0.22 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.44→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 50 188 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221808
X-RAY DIFFRACTIONr_bond_other_d0.0010.021727
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9962486
X-RAY DIFFRACTIONr_angle_other_deg0.66534008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70325.16162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09615292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.237158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022063
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
X-RAY DIFFRACTIONr_nbd_refined0.2080.3282
X-RAY DIFFRACTIONr_nbd_other0.1940.31772
X-RAY DIFFRACTIONr_nbtor_refined0.1750.5822
X-RAY DIFFRACTIONr_nbtor_other0.0880.51049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.5255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.330
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.390
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.542
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9621.51494
X-RAY DIFFRACTIONr_mcbond_other0.2211.5481
X-RAY DIFFRACTIONr_mcangle_it1.221902
X-RAY DIFFRACTIONr_scbond_it1.8863702
X-RAY DIFFRACTIONr_scangle_it2.6434.5584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 124 -
Rwork0.182 2351 -
obs--100 %

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