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- PDB-5e5j: Joint X-ray/neutron structure of HIV-1 protease triple mutant (V3... -

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Basic information

Entry
Database: PDB / ID: 5e5j
TitleJoint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with darunavir at pH 6.0
ComponentsProtease
Keywordshydrolase/hydrolase inhibitor / protease HIV-1 drug resistant mutant inhibitor complex / hydrolase-hydrolase inhibitor complex
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
Chem-017 / DEUTERATED WATER / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKovalevsky, A.Y. / Gerlits, O.O.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.
Authors: Gerlits, O. / Wymore, T. / Das, A. / Shen, C.H. / Parks, J.M. / Smith, J.C. / Weiss, K.L. / Keen, D.A. / Blakeley, M.P. / Louis, J.M. / Langan, P. / Weber, I.T. / Kovalevsky, A.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_CSD ..._chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0573
Polymers21,5092
Non-polymers5481
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-1 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.724, 87.257, 46.547
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 Protease


Mass: 10754.703 Da / Num. of mol.: 2 / Mutation: Q7K, V32I, L33I, I47V, L63I, C67A, V82I, C95A
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-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37N3O7S / Comment: medication, antiretroviral*YM
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
Method
X-RAY DIFFRACTION
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: NaCl, MES / PH range: 6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORLADI/ILL22.80 - 4.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEAug 20, 2014OSMIC VARIMAX
MAATEL IMAGINE2IMAGE PLATEOct 13, 2014COLLIMATORS
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: 5E5J

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.85-402110298.23.90.048126.5
2-27.611317083.55.90.14725.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible allDiffraction-ID
1.85-1.923.90.4782.896.3
2-2.115.20.2673.270.12

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
nCNS1.0.0refinement
LAUEGENdata reduction
LSCALEdata scaling
Refinement

Biso max: 88.94 Å2 / Biso mean: 27.3 Å2 / Biso min: 8.34 Å2 / % reflection Rfree: 5 % / R Free selection details: RANDOM / Diffraction-ID: 1 / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 4JEC

4jec

/ Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)Bsol (Å2)ksol (e/Å3)
1.85-20X-RAY DIFFRACTION0.2010.19492617456214261833987.943.11720.295004
2-40NEUTRON DIFFRACTION0.2450.21756411729161281172968.837.03230.521646
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.230.2
Luzzati d res low-5
Luzzati sigma a0.170.15
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.290.25
Luzzati d res low-5
Luzzati sigma a0.480.43
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 38 116 1668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_torsion_deg16.4
X-RAY DIFFRACTIONc_torsion_impr_deg0.85
NEUTRON DIFFRACTIONc_bond_d0.008
NEUTRON DIFFRACTIONc_angle_deg1
NEUTRON DIFFRACTIONc_torsion_deg16.4
NEUTRON DIFFRACTIONc_torsion_impr_deg0.85
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 (%)
1.85-1.930.2576450.2221425X-RAY DIFFRACTION0.0322642142553.9
1.93-2.040.198904.60.2111877X-RAY DIFFRACTION0.0212632196774.7
2.04-2.160.2261064.70.2112127X-RAY DIFFRACTION0.0222646223384.4
2.16-2.330.2421345.70.2142225X-RAY DIFFRACTION0.0212638235989.4
2.33-2.570.2791144.70.2152302X-RAY DIFFRACTION0.0262668241690.6
2.57-2.940.2261104.30.2142427X-RAY DIFFRACTION0.0222684253794.5
2.94-3.70.1781234.70.192508X-RAY DIFFRACTION0.0162701263197.4
3.7-36.710.1721575.60.1692629X-RAY DIFFRACTION0.0142846278697.9
2-2.130.3895450.359988NEUTRON DIFFRACTION0.053198798849.7
2.13-2.240.308605.40.3111057NEUTRON DIFFRACTION0.041974111756.6
2.24-2.380.336604.80.2761194NEUTRON DIFFRACTION0.0431978125463.4
2.38-2.570.287584.40.2461270NEUTRON DIFFRACTION0.0381999132866.4
2.57-2.830.28724.80.2191435NEUTRON DIFFRACTION0.0331998150775.4
2.83-3.230.221724.30.1921593NEUTRON DIFFRACTION0.0262009166582.9
3.23-4.070.207955.10.1671766NEUTRON DIFFRACTION0.0212038186191.3
4.07-28.250.181145.70.1751895NEUTRON DIFFRACTION0.0172160200993

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