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- PDB-5t8h: Joint X-ray/neutron structure of HIV-1 protease triple mutant (V3... -

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Basic information

Entry
Database: PDB / ID: 5t8h
TitleJoint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with amprenavir at pH 6.0
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / aspartic protease drug resistant mutant amprenavir / 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-478 / DEUTERATED WATER / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKovalevsky, A.Y. / Gerlits, O.O.
Citation
Journal: J. Med. Chem. / Year: 2017
Title: Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K.
Authors: Gerlits, O. / Keen, D.A. / Blakeley, M.P. / Louis, J.M. / Weber, I.T. / Kovalevsky, A.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2009
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
History
DepositionSep 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0153
Polymers21,5092
Non-polymers5061
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21200 Å2
ΔGint52 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.234, 87.359, 46.565
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-478 / {3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER / Amprenavir / Amprenavir


Mass: 505.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35N3O6S / Comment: protease inhibitor, medication*YM
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 1M NaCl, 0.1 M NaMES / PH range: 6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORLADILADI/ILL22.8-4.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEMar 3, 2016OSMIC VARIMAX
MAATEL IMAGINE2IMAGE PLATEFeb 22, 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: 5T8H

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.85-402050595.940.046126.1
2.2-40893374.43.90.16727.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.85-1.924.10.4652.7193.8
2.2-2.323.40.3084254.5

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Processing

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

Biso mean: 27.93 Å2 / Biso min: 8.16 Å2 / % reflection Rfree: 5 % / R Free selection details: RANDOM / 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 / Bsol: 52.111 Å2 / ksol: 0.301255 e/Å3

Resolution (Å)Refine-IDBiso max (Å2)Rfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obs% reflection obs (%)Diffraction-ID
1.85-36.61X-RAY DIFFRACTION82.60.2140.0070.191885212831804084.81
2.2-33.76NEUTRON DIFFRACTION84.830.2550.21739712268839465.62
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.220.2
Luzzati d res low-5
Luzzati sigma a0.160.14
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.360.3
Luzzati d res low-5
Luzzati sigma a0.570.48
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 1.85→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 35 124 1673
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg15.3
X-RAY DIFFRACTIONx_torsion_impr_deg0.87
NEUTRON DIFFRACTIONx_bond_d0.009
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg15.3
NEUTRON DIFFRACTIONx_torsion_impr_deg0.87
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 (%)
1.85-1.930.2717550.2131213X-RAY DIFFRACTION0.0312620128849.2
1.93-2.040.254965.20.2041739X-RAY DIFFRACTION0.0262616183570.1
2.04-2.160.21934.40.2042022X-RAY DIFFRACTION0.0222625211580.6
2.16-2.330.2211124.90.2092171X-RAY DIFFRACTION0.0212620228387.1
2.33-2.570.2391335.60.2172235X-RAY DIFFRACTION0.0212647236889.5
2.57-2.940.221134.60.2072323X-RAY DIFFRACTION0.0212662243691.5
2.94-3.70.2161254.90.1932443X-RAY DIFFRACTION0.0192693256895.4
3.7-36.610.1871294.80.1642553X-RAY DIFFRACTION0.0162829268294.8
2.2-2.330.443050.352694NEUTRON DIFFRACTION0.043150169446.2
2.33-2.460.311415.30.332737NEUTRON DIFFRACTION0.049151877851.2
2.46-2.610.394576.60.316813NEUTRON DIFFRACTION0.052149987058
2.61-2.810.314373.90.282911NEUTRON DIFFRACTION0.052150394863.1
2.81-3.10.301494.70.253996NEUTRON DIFFRACTION0.0431523104568.6
3.1-3.540.194524.30.1751162NEUTRON DIFFRACTION0.0271528121479.5
3.54-4.460.17574.10.151330NEUTRON DIFFRACTION0.0231557138789
4.46-33.760.194745.10.1631384NEUTRON DIFFRACTION0.0231644145888.7

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