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- PDB-7lec: HIV-1 Protease WT (NL4-3) in Complex with PU3 (LR3-69) -

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Basic information

Entry
Database: PDB / ID: 7lec
TitleHIV-1 Protease WT (NL4-3) in Complex with PU3 (LR3-69)
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV / NL4-3 PROTEASE / PROTEASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / 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
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLockbaum, G.J. / Rusere, L.N. / Henes, M. / Kosovrasti, K. / Lee, S.K. / Spielvogel, E. / Nalivaika, E.A. / Swanstrom, R. / KurtYilmaz, N. / Schiffer, C.A. / Ali, 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 Inhibitors with a P1 Phosphonate Modification Maintain Potency against Drug Resistant Variants by Increased van der Waals Contacts with Flaps Residues
Authors: Lockbaum, G.J. / Rusere, L.N. / Henes, M. / Kosovrasti, K. / Lee, S.K. / Spielvogel, E. / Nalivaika, E.A. / Swanstrom, R. / KurtYilmaz, N. / Schiffer, C.A. / Ali, A.
History
DepositionJan 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 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

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Assembly

Deposited unit
B: Protease
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5995
Polymers21,6642
Non-polymers9353
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-46 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.361, 58.591, 61.740
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 6 or (resid 7...
21(chain B and (resid 1 through 44 or (resid 45...

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
11PROPROTRPTRP(chain A and (resid 1 through 6 or (resid 7...AB1 - 61 - 6
12LYSLYSLYSLYS(chain A and (resid 1 through 6 or (resid 7...AB77
13PROPROPHEPHE(chain A and (resid 1 through 6 or (resid 7...AB1 - 991 - 99
14PROPROPHEPHE(chain A and (resid 1 through 6 or (resid 7...AB1 - 991 - 99
15PROPROPHEPHE(chain A and (resid 1 through 6 or (resid 7...AB1 - 991 - 99
21PROPROPROPRO(chain B and (resid 1 through 44 or (resid 45...BA1 - 441 - 44
22LYSLYSLYSLYS(chain B and (resid 1 through 44 or (resid 45...BA4545
23PROPROPHEPHE(chain B and (resid 1 through 44 or (resid 45...BA1 - 991 - 99

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Components

#1: Protein Protease


Mass: 10831.833 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ULI9
#2: Chemical ChemComp-XVP / diethyl ({4-[(2S,3R)-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxy-4-({[4-(hydroxymethyl)phenyl]sulfonyl}[(2S)-2-methylbutyl]amino)butyl]phenoxy}methyl)phosphonate


Mass: 742.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H51N2O12PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 42.63 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.94→23.72 Å / Num. obs: 14216 / % possible obs: 99 % / Redundancy: 7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 25.3
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 686 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASERphasing
PHENIX1.15.2_3472refinement
Cootmodel building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DGX

6dgx


Resolution: 1.94→23.711 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 715 5.04 %
Rwork0.1992 13459 -
obs0.2016 14174 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.38 Å2 / Biso mean: 32.1392 Å2 / Biso min: 13.74 Å2
Refinement stepCycle: final / Resolution: 1.94→23.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 109 155 1752
Biso mean--36.35 36.88 -
Num. residues----198
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A596X-RAY DIFFRACTION7.179TORSIONAL
12B596X-RAY DIFFRACTION7.179TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.94-2.08950.28741380.2085259198
2.0895-2.29960.28431380.191264899
2.2996-2.6320.22331430.198266499
2.632-3.31460.25081430.2062718100
3.3146-23.7110.23621530.19662838100

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