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- PDB-1ztz: Crystal structure of HIV protease- metallacarborane complex -

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Basic information

Entry
Database: PDB / ID: 1ztz
TitleCrystal structure of HIV protease- metallacarborane complex
Components
  • PROTEASE RETROPEPSIN
  • autoproteolytic tetrapeptide
KeywordsHYDROLASE / rational drug design / HIV protease inhibitors / aspartic proteases / carboranes / metallacarboranes
Function / homology
Function and homology information


RNA stem-loop binding / host cell / 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 ...RNA stem-loop binding / host cell / 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 / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / 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 / virion membrane / structural molecule activity / 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 / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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
COBALT BIS(1,2-DICARBOLLIDE) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCigler, P. / Kozisek, M. / Rezacova, P. / Brynda, J. / Otwinowski, Z. / Sedlacek, J. / Bodem, J. / Kraeusslich, H.-G. / Kral, V. / Konvalinka, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: From nonpeptide toward noncarbon protease inhibitors: Metallacarboranes as specific and potent inhibitors of HIV protease
Authors: Cigler, P. / Kozisek, M. / Rezacova, P. / Brynda, J. / Otwinowski, Z. / Pokorna, J. / Plesek, J. / Gruner, B. / Doleckova-Maresova, L. / Masa, M. / Sedlacek, J. / Bodem, J. / Kraeusslich, H.- ...Authors: Cigler, P. / Kozisek, M. / Rezacova, P. / Brynda, J. / Otwinowski, Z. / Pokorna, J. / Plesek, J. / Gruner, B. / Doleckova-Maresova, L. / Masa, M. / Sedlacek, J. / Bodem, J. / Kraeusslich, H.-G. / Kral, V. / Konvalinka, J.
History
DepositionMay 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 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.end_auth_comp_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
P: autoproteolytic tetrapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5455
Polymers21,8983
Non-polymers6472
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-28 kcal/mol
Surface area10450 Å2
MethodPISA
2
A: PROTEASE RETROPEPSIN
B: PROTEASE RETROPEPSIN
P: autoproteolytic tetrapeptide
hetero molecules

A: PROTEASE RETROPEPSIN
B: PROTEASE RETROPEPSIN
P: autoproteolytic tetrapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,09110
Polymers43,7966
Non-polymers1,2954
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area12460 Å2
ΔGint-95 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.321, 67.181, 42.498
Angle α, β, γ (deg.)90.00, 94.99, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1065-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVALAA1 - 321 - 32
21PROPROVALVALBB1 - 321 - 32
12ILEILEPHEPHEAA63 - 9963 - 99
22ILEILEPHEPHEBB63 - 9963 - 99

NCS ensembles :
ID
1
2
Detailsbiologically active unit is HIV PR dimer

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Components

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


Mass: 10804.808 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / 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: Protein/peptide autoproteolytic tetrapeptide


Mass: 288.300 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CB5 / COBALT BIS(1,2-DICARBOLLIDE)


Mass: 323.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H22B18Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.45 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 2.0M Ammonium dihydrogen Phospate, 0.1M Tric.Cl pH 8.5, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 23, 2004
Details: Flat pre-mirror, a fixed-exit sagital focusing double Silicon (111) crystal monochromator and a vertical focusing mirror. Both mirrors are Rhodium-coated.
RadiationMonochromator: Silicon (111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 12431 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.3
Reflection shellResolution: 2.14→2.19 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1nh0

1nh0


Resolution: 2.15→28.81 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.72 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23258 642 4.9 %RANDOM
Rwork0.17592 ---
obs0.17864 12431 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.384 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.05 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.323 Å
Refinement stepCycle: LAST / Resolution: 2.15→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 46 202 1768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221671
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9292.1262441
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5555199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.89825.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48515280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.26156
X-RAY DIFFRACTIONr_chiral_restr0.8840.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021158
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2760
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21066
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9251.51010
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51321609
X-RAY DIFFRACTIONr_scbond_it2.6743720
X-RAY DIFFRACTIONr_scangle_it4.134.5580
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1245medium positional0.420.5
2272medium positional0.350.5
1245medium thermal1.172
2272medium thermal1.152
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 42 -
Rwork0.249 891 -
obs--100 %
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)
11.95040.63070.2574.5756-5.033510.34460.0304-0.11470.0014-0.0620.13370.4740.3639-0.6573-0.164-0.184-0.0218-0.006-0.05250.0025-0.173321.742-0.1332.931
22.83470.63320.1084.5276-4.78811.71560.06050.10850.0846-0.49120.16830.33960.7135-0.6359-0.2288-0.125-0.0227-0.0236-0.07760.0054-0.2121.8130.902-3.191
33.6704-1.3678-1.53925.14-2.10935.23940.1741-0.03710.1618-0.0745-0.2255-0.35570.00150.14080.0513-0.151-0.0555-0.0315-0.11210.0122-0.162328.956-4.88911.944
41.6229-0.45011.34065.8238-1.37994.84640.08020.00240.0422-0.6192-0.179-0.5590.17140.1650.0989-0.10660.05030.0524-0.09110.0346-0.109928.5356.409-11.894
511.78142.2966-5.16882.148-1.45113.8735-0.1883-0.6203-1.0502-0.1682-0.1576-0.37210.51570.48880.346-0.20250.0609-0.0801-0.13620.0665-0.03739.885-11.55511.786
67.295-0.47520.323221.0830.13671.6213-0.18140.22950.745-0.5821-0.3796-4.6392-0.05760.41680.5609-0.08440.04560.1681-0.04330.17980.893539.07314.09-12.166
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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