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- PDB-7m9l: HIV-1 Protease WT (NL4-3) in Complex with LR4-15 -

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Basic information

Entry
Database: PDB / ID: 7m9l
TitleHIV-1 Protease WT (NL4-3) in Complex with LR4-15
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV / NL4-3 PROTEASE / DRUG RESISTANCE / PROTEASE INHIBITOR / COMPLEX / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-YTY / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsLockbaum, G.J. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM109767 United States
CitationJournal: To Be Published
Title: HIV-1 Protease WT (NL4-3) in Complex with LR4-15
Authors: Lockbaum, G.J. / Schiffer, C.A.
History
DepositionMar 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protease
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6275
Polymers21,6642
Non-polymers9633
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-47 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.212, 59.055, 61.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 20 or (resid 21...
21(chain B and (resid 1 through 6 or (resid 7...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLYSLYS(chain A and (resid 1 through 20 or (resid 21...AB1 - 201 - 20
12GLUGLUALAALA(chain A and (resid 1 through 20 or (resid 21...AB21 - 2221 - 22
13PROPROPHEPHE(chain A and (resid 1 through 20 or (resid 21...AB1 - 991 - 99
14PROPROPHEPHE(chain A and (resid 1 through 20 or (resid 21...AB1 - 991 - 99
15PROPROPHEPHE(chain A and (resid 1 through 20 or (resid 21...AB1 - 991 - 99
16PROPROPHEPHE(chain A and (resid 1 through 20 or (resid 21...AB1 - 991 - 99
21PROPROTRPTRP(chain B and (resid 1 through 6 or (resid 7...BA1 - 61 - 6
22LYSLYSLYSLYS(chain B and (resid 1 through 6 or (resid 7...BA77
23PROPROPHEPHE(chain B and (resid 1 through 6 or (resid 7...BA1 - 991 - 99

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Components

#1: Protein Protease / PR / Retropepsin


Mass: 10831.833 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-YTY / diethyl [(4-{(2S,3R)-4-[(2-ethylbutyl){4-[(1S)-1-hydroxyethyl]benzene-1-sulfonyl}amino]-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxybutyl}phenoxy)methyl]phosphonate


Mass: 770.867 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H55N2O12PS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 23-24% (w/v) Ammonium Sulfate, 0.1M Bis-Tris-Methane-HCl Buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 1.75→42.661 Å / Num. obs: 18787 / % possible obs: 97.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 25.8
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1822

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.14_3260refinement
Cootmodel building
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DGX

6dgx


Resolution: 1.752→42.661 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 939 5.01 %
Rwork0.1769 17814 -
obs0.1788 18753 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.85 Å2 / Biso mean: 26.678 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: final / Resolution: 1.752→42.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 117 158 1743
Biso mean--28.24 34.73 -
Num. residues----198
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A596X-RAY DIFFRACTION8.844TORSIONAL
12B596X-RAY DIFFRACTION8.844TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.752-1.84390.26091290.2011233991
1.8439-1.95950.24891380.1884251297
1.9595-2.11070.24951170.1725251696
2.1107-2.32310.21121400.173252398
2.3231-2.65930.24311350.1755257798
2.6593-3.35020.2181360.1763261298
3.3502-42.660.18751440.175273598

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