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- PDB-6ptp: Joint X-ray/neutron structure of HIV-1 protease triple mutant (V3... -

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Basic information

Entry
Database: PDB / ID: 6ptp
TitleJoint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with tetrahedral intermediate mimic KVS-1
ComponentsHIV-1 Protease
KeywordsHYDROLASE / HIV-1 protease / aspartic protease / homodimer
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis / identical protein binding
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DEUTERATED WATER / Chem-KVS / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 1.85 Å
AuthorsKovalevsky, A. / Das, A.
CitationJournal: Acs Omega / Year: 2020
Title: Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design.
Authors: Kumar, M. / Mandal, K. / Blakeley, M.P. / Wymore, T. / Kent, S.B.H. / Louis, J.M. / Das, A. / Kovalevsky, A.
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 Protease
B: HIV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3103
Polymers21,5092
Non-polymers8011
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.497, 87.400, 46.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HIV-1 Protease /


Mass: 10754.703 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A, V32I, I47V and V82I
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: Q7SSI0
#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


Mass: 800.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H68N10O10 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, 1.0 M NaCl, pH 6.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.541.54
NUCLEAR REACTORLADI III22.80-4.02.80-4.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEOct 5, 2016osmic varimax
MAATEL2IMAGE PLATEOct 5, 2016collimators
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.81
341
Reflection

Entry-ID: 6PTP

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.85-402094297.63.90.049125.3
2.2-40966677.33.10.16927.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.85-1.923.80.4893196
2.2-2.323.20.3273.4264.6

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Processing

SoftwareName: nCNS / Version: 1.0.0 / Classification: refinement
Refinement

% reflection Rfree: 5 % / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Stereochemistry target values: JOINT X-RAY/NEUTRON ML

Starting modelResolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection obs% reflection obs (%)Diffraction-IDIsotropic thermal model
3DCR

3dcr

1.85-40X-RAY DIFFRACTION76.8727.186.860.2170.1929321884787.61
2.2-40NEUTRON DIFFRACTION0.2570.234429884067.92NULL
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.230.2
Luzzati d res low-5
Luzzati sigma a0.130.13
Luzzati d res high-1.85
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.360.31
Luzzati d res low-5
Luzzati sigma a0.530.44
Luzzati d res high-2.21
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 56 104 1674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg18.2
X-RAY DIFFRACTIONx_torsion_impr_deg1.11
NEUTRON DIFFRACTIONx_bond_d0.017
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_torsion_deg18.2
NEUTRON DIFFRACTIONx_torsion_impr_deg1.11
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.85-1.940.266950.2251465X-RAY DIFFRACTION0.0312645153458
1.94-2.040.211125.40.1971954X-RAY DIFFRACTION0.022652206677.9
2.04-2.160.2521044.60.2062144X-RAY DIFFRACTION0.0252636224885.3
2.16-2.330.2161325.60.2042238X-RAY DIFFRACTION0.0192649237089.4
2.33-2.570.2231174.80.2132333X-RAY DIFFRACTION0.0212672245091.7
2.57-2.940.2591154.50.2182432X-RAY DIFFRACTION0.0242691254794.6
2.94-3.70.2511264.80.192520X-RAY DIFFRACTION0.0222712264697.5
3.7-36.820.1731455.40.1642540X-RAY DIFFRACTION0.0142853268594.1
2.21-2.310.412435.50.357739NEUTRON DIFFRACTION0.063156278250.1
2.31-2.430.365394.70.334798NEUTRON DIFFRACTION0.058155083754
2.43-2.590.336374.10.307855NEUTRON DIFFRACTION0.055157789256.6
2.59-2.790.312484.90.273939NEUTRON DIFFRACTION0.045156398763.1
2.79-3.070.296544.90.2611050NEUTRON DIFFRACTION0.041571110470.3
3.07-3.510.207544.30.1981203NEUTRON DIFFRACTION0.0281600125778.5
3.51-4.420.231694.80.1951360NEUTRON DIFFRACTION0.0281613142988.6
4.42-28.160.179815.30.1761435NEUTRON DIFFRACTION0.021703151689

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