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- PDB-3nxn: X-ray structure of ester chemical analogue 'covalent dimer' [Ile5... -

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Basic information

Entry
Database: PDB / ID: 3nxn
TitleX-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor
Componentsprotease covalent dimer
Keywordshydrolase/hydrolase inhibitor / beta-barrel / hydrolase-hydrolase inhibitor complex
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
N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide / Chem-KVS / Gag-Pol polyprotein
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTorbeev, V.Y. / Kent, S.B.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.
Authors: Torbeev, V.Y. / Raghuraman, H. / Hamelberg, D. / Tonelli, M. / Westler, W.M. / Perozo, E. / Kent, S.B.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 2.0Jul 31, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.type / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protease covalent dimer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0786
Polymers21,8931
Non-polymers1,1855
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.871, 57.644, 61.640
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 covalent dimer


Mass: 21892.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical protein synthesis / References: UniProt: P03369*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-KVS / N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide


Type: Peptide-like / Class: Inhibitor / Mass: 800.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H68N10O10
References: N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Citrate, 0.2 M Sodium Phosphate, 30% (w/v) Ammonium Sulfate, 10% (v/v) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2007
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17520 / % possible obs: 99.7 % / Observed criterion σ(F): 102.9 / Observed criterion σ(I): 102.9 / Redundancy: 5.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 22.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4.51 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.822 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22511 885 5.1 %RANDOM
Rwork0.19351 ---
obs0.19513 16574 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 mean: 20.292 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2--0.11 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 76 98 1717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221639
X-RAY DIFFRACTIONr_bond_other_d0.0010.021094
X-RAY DIFFRACTIONr_angle_refined_deg1.8072.0052216
X-RAY DIFFRACTIONr_angle_other_deg0.92832693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9935199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.06424.91559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45215284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.425159
X-RAY DIFFRACTIONr_chiral_restr0.1120.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
X-RAY DIFFRACTIONr_nbd_refined0.210.2246
X-RAY DIFFRACTIONr_nbd_other0.2060.21101
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2759
X-RAY DIFFRACTIONr_nbtor_other0.0930.2896
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1680.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.171.51049
X-RAY DIFFRACTIONr_mcbond_other0.3291.5429
X-RAY DIFFRACTIONr_mcangle_it1.83421655
X-RAY DIFFRACTIONr_scbond_it2.5843659
X-RAY DIFFRACTIONr_scangle_it4.1634.5558
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 50 -
Rwork0.198 1141 -
obs--94.82 %
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)
11.4158-0.31060.58470.79180.15270.8416-0.03570.07120.0111-0.01950.0522-0.0021-0.02410.0687-0.0164-0.0379-0.0137-0.0032-0.056-0.0018-0.05045.04361.168218.3173
216.9913-13.251218.475712.9251-15.954725.83840.13340.29660.0612-0.6249-0.4069-0.27490.43770.64790.2735-0.033-0.01850.0207-0.0058-0.0185-0.03535.4503-0.804613.1496
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 202
2X-RAY DIFFRACTION2A204

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