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- PDB-3bva: Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analo... -

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Basic information

Entry
Database: PDB / ID: 3bva
TitleCystal structure of HIV-1 Active Site Mutant D25N and p2-NC analog inhibitor
ComponentsProtease (Retropepsin)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / DRUG RESISTANCE / HIV-1 / 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 / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / 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 / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / Chem-2NC / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.05 Å
AuthorsLiu, F. / Weber, I.T.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Effect of the Active Site D25N Mutation on the Structure, Stability, and Ligand Binding of the Mature HIV-1 Protease.
Authors: Sayer, J.M. / Liu, F. / Ishima, R. / Weber, I.T. / Louis, J.M.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor.
Authors: Ishima, R. / Torchia, D.A. / Lynch, S.M. / Gronenborn, A.M. / Louis, J.M.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and G73S.
Authors: Liu, F. / Boross, P.I. / Wang, Y.F. / Tozser, J. / Louis, J.M. / Harrison, R.W. / Weber, I.T.
History
DepositionJan 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Oct 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 1.4Aug 30, 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 (Retropepsin)
B: Protease (Retropepsin)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5276
Polymers21,4792
Non-polymers1,0474
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-23.2 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.196, 85.893, 46.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1157-

HOH

21A-1215-

HOH

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Components

#1: Protein Protease (Retropepsin) / (PR)


Mass: 10739.691 Da / Num. of mol.: 2 / Mutation: Q7K, D25N, L33I, L63I, C67A, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: GAG-POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-2NC / N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / p2/NC


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 770.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68N11O8
References: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR 2NC IS A P2/NC ANALOG. IT HAS A REDUCED PEPTIDE BOND ISOSTERE [CH2-NH] IN PLACE OF ...THE INHIBITOR 2NC IS A P2/NC ANALOG. IT HAS A REDUCED PEPTIDE BOND ISOSTERE [CH2-NH] IN PLACE OF THE SCISSILE AMIDE

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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: 2.63 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 10% SODIUM CHLORIDE, CITRATE-PHOSPHATE BUFFER, 7-8% DMSO, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2000
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. all: 102685 / Num. obs: 97551 / % possible obs: 94.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 22.3
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 82.1

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB entry 1DAZ

1daz


Resolution: 1.05→10 Å / Num. parameters: 17901 / Num. restraintsaints: 23143 / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.18 5134 5 %RANDOM
Rwork0.15 ---
obs0.1548 97551 94 %-
all-102685 --
Refine analyzeNum. disordered residues: 37 / Occupancy sum hydrogen: 1663.41 / Occupancy sum non hydrogen: 1775.83
Refinement stepCycle: LAST / Resolution: 1.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 72 234 1818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0309
X-RAY DIFFRACTIONs_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.114
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.062
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0.096

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