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- PDB-2pym: HIV-1 PR mutant in complex with nelfinavir -

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Basic information

Entry
Database: PDB / ID: 2pym
TitleHIV-1 PR mutant in complex with nelfinavir
ComponentsPROTEASE RETROPEPSIN
KeywordsHYDROLASE / resistance / nelfinavir
Function / homology
Function and homology information


HIV-1 retropepsin / 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 / viral penetration into host nucleus ...HIV-1 retropepsin / 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 / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-1UN / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRezacova, P. / Kozisek, M. / Saskova, K. / Brynda, J. / Konvalinka, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Molecular analysis of the HIV-1 resistance development: enzymatic activities, crystal structures, and thermodynamics of nelfinavir-resistant HIV protease mutants
Authors: Kozisek, M. / Bray, J. / Rezacova, P. / Saskova, K. / Brynda, J. / Pokorna, J. / Mammano, F. / Rulisek, L. / Konvalinka, J.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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_seq_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_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
A: PROTEASE RETROPEPSIN
B: PROTEASE RETROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0033
Polymers21,4352
Non-polymers5681
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.218, 62.218, 81.415
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A B
21A

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHE5AA1 - 991 - 99
12PROPROPHEPHE5BB1 - 991 - 99
211UN1UN1UN1UN4AC1001
Detailsthe biological assembly is dimer

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Components

#1: Protein PROTEASE RETROPEPSIN / E.C.3.4.23.16 / HIV-1 PROTEASE


Mass: 10717.640 Da / Num. of mol.: 2 / Mutation: D30N, N88D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: type B / Gene: gag-pol / Plasmid: pET like, T7 promotor driven / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-1UN / 2-[2-HYDROXY-3-(3-HYDROXY-2-METHYL-BENZOYLAMINO)-4-PHENYL SULFANYL-BUTYL]-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID TERT-BUTYLAMIDE / NELFINAVIR MESYLATE AG1343


Mass: 567.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H45N3O4S / Comment: medication, antiretroviral, protease inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: reservoir solution: 0.5M (NH4)2SO4, 0.1M MES pH 5.4 or pH 5.5; drops: 2+1ul (protein+reservoir}; protein: 3-5mg/ml 5-fold molar excess of inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 2, 2005 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→54.23 Å / Num. obs: 16412 / % possible obs: 98.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 7.2
Reflection shellResolution: 1.8→1.89 Å / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 2.4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8G

1u8g


Resolution: 1.9→54.23 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.126 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.199 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24378 699 5 %RANDOM
Rwork0.1927 ---
obs0.19523 13217 98.46 %-
all-13217 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.574 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 40 138 1682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2782.0422258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5025208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.17725.18554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0515286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.358156
X-RAY DIFFRACTIONr_chiral_restr0.090.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021180
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.2774
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21121
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5881.51036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94121620
X-RAY DIFFRACTIONr_scbond_it1.2963716
X-RAY DIFFRACTIONr_scangle_it2.0794.5632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDNumberTypeRms dev position (Å)Weight position
1396medium positional0.050.5
240medium positional0.050.5
1355loose positional0.355
1396medium thermal0.192
240medium thermal0.182
1355loose thermal0.4910
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 61 -
Rwork0.235 973 -
obs--99.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.3954.07431.56787.08071.153218.7631-0.3217-0.45641.0317-0.0119-0.04540.617-1.4204-1.21920.3671-0.16960.0586-0.1063-0.0815-0.0519-0.1244-18.40226.27225.678
29.67660.83312.01723.11540.763618.9798-0.3522-0.00981.0082-0.41-0.10840.4912-1.8109-0.65510.4606-0.057-0.0145-0.1146-0.1838-0.0826-0.112-13.54529.06628.088
313.34385.52415.41543.06423.14135.1126-0.29190.40540.1594-0.34030.16650.157-0.2770.25480.1254-0.2286-0.037-0.0275-0.226-0.0177-0.2391-20.08315.99118.066
410.45387.35615.06526.07012.98674.91220.0827-0.5810.2330.1791-0.21880.05760.0937-0.36330.136-0.2562-0.0163-0.0347-0.1944-0.0178-0.2564-3.79825.38535.698
518.9379-1.85356.94845.7711-1.1428.45750.33842.7585-1.791-0.62320.235-0.15320.27491.4174-0.5734-0.0720.02480.03290.2334-0.31550.0401-11.5668.85812.928
67.41654.24791.813519.41376.49997.52421.0763-1.1187-0.92352.3487-0.6763-1.41721.392-0.4296-0.40.1625-0.116-0.27110.00840.18370.0262-1.79914.41440.843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 91 - 9
2X-RAY DIFFRACTION1AA86 - 9986 - 99
3X-RAY DIFFRACTION2BB1 - 91 - 9
4X-RAY DIFFRACTION2BB86 - 9986 - 99
5X-RAY DIFFRACTION3AA10 - 3210 - 32
6X-RAY DIFFRACTION3AA63 - 8563 - 85
7X-RAY DIFFRACTION4BB10 - 3210 - 32
8X-RAY DIFFRACTION4BB63 - 8563 - 85
9X-RAY DIFFRACTION5AA33 - 6233 - 62
10X-RAY DIFFRACTION6BB33 - 6233 - 62

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