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- PDB-7wcq: Crystal structure of HIV-1 protease in complex with lactam deriva... -

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Basic information

Entry
Database: PDB / ID: 7wcq
TitleCrystal structure of HIV-1 protease in complex with lactam derivative 1
ComponentsProtease
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-Inhibitor complex
Function / homology
Function and homology information


viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function
Retropepsin-like catalytic domain / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. ...Retropepsin-like catalytic domain / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-8OC / Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.011 Å
AuthorsKojima, E. / Iimuro, A. / Nakajima, M. / Kinuta, H. / Asada, N. / Sako, Y. / Nakata, Z. / Uemura, K. / Arita, S. / Miki, S. ...Kojima, E. / Iimuro, A. / Nakajima, M. / Kinuta, H. / Asada, N. / Sako, Y. / Nakata, Z. / Uemura, K. / Arita, S. / Miki, S. / Wakasa-Morimoto, C. / Tachibana, Y. / Fumoto, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Pocket-to-Lead: Structure-Based De Novo Design of Novel Non-peptidic HIV-1 Protease Inhibitors Using the Ligand Binding Pocket as a Template.
Authors: Kojima, E. / Iimuro, A. / Nakajima, M. / Kinuta, H. / Asada, N. / Sako, Y. / Nakata, Z. / Uemura, K. / Arita, S. / Miki, S. / Wakasa-Morimoto, C. / Tachibana, Y.
History
DepositionDec 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3142
Polymers10,8311
Non-polymers4841
Water70339
1
A: Protease
hetero molecules

A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6294
Polymers21,6622
Non-polymers9672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area4040 Å2
ΔGint-21 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.702, 62.702, 81.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Protease / Retropepsin


Mass: 10830.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WFL7
#2: Chemical ChemComp-8OC / (3R,4R)-3-[(4-fluorophenyl)methyl]-1-[(4-methoxyphenyl)methyl]-3-(4-methylsulfonylphenyl)-4-oxidanyl-pyrrolidin-2-one


Mass: 483.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26FNO5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-Tris pH 6.5 and 0.5 M Magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 6745 / % possible obs: 99.4 % / Redundancy: 10.4 % / Biso Wilson estimate: 24.14 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.019 / Rrim(I) all: 0.062 / Χ2: 0.907 / Net I/σ(I): 16.8 / Num. measured all: 69831
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.01-2.0810.30.2676520.9790.0860.2810.921100
2.08-2.1710.40.26540.9840.0640.2110.919100
2.17-2.2610.40.1566580.9920.050.1640.945100
2.26-2.3810.50.1396510.9920.0440.1470.912100
2.38-2.5310.50.116700.9950.0350.1150.919100
2.53-2.7310.40.096730.9960.0290.0950.956100
2.73-310.60.0726650.9970.0230.0760.97699.8
3-3.4410.50.0566820.9980.0180.0590.91299.4
3.44-4.3310.40.0446880.9990.0140.0460.84398.9
4.33-509.60.0387520.9990.0120.040.77396.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.49
Highest resolutionLowest resolution
Rotation32.66 Å5 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.11.1-2575-000refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LL3

4ll3


Resolution: 2.011→32.657 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 345 5.12 %
Rwork0.2183 6390 -
obs0.2206 6735 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.51 Å2 / Biso mean: 25.1778 Å2 / Biso min: 10.07 Å2
Refinement stepCycle: final / Resolution: 2.011→32.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 34 39 810
Biso mean--22.99 28.44 -
Num. residues----99
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007786
X-RAY DIFFRACTIONf_angle_d0.9531074
X-RAY DIFFRACTIONf_chiral_restr0.072127
X-RAY DIFFRACTIONf_plane_restr0.005132
X-RAY DIFFRACTIONf_dihedral_angle_d10.25454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.011-2.53350.31951790.24753099100
2.5335-32.6570.24051660.2071329199

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