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- PDB-3ka2: Crystal structure of chemically synthesized 203 amino acid 'coval... -

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Basic information

Entry
Database: PDB / ID: 3ka2
TitleCrystal structure of chemically synthesized 203 amino acid 'covalent dimer' [L-Ala;Gly51']HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor at 1.4 A resolution
Components[L-Ala51;Gly51']HIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta-barrel / 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 / RNA-directed DNA polymerase / viral genome integration into host DNA / 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 / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / telomerase activity / RNA stem-loop binding / 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 / viral translational frameshifting / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / 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. / 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. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molrep v.5 / Resolution: 1.4 Å
AuthorsTorbeev, V.Y. / Kent, S.B.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.
Authors: Torbeev, V.Y. / Raghuraman, H. / Hamelberg, D. / Tonelli, M. / Westler, W.M. / Perozo, E. / Kent, S.B.
History
DepositionOct 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Sep 12, 2012Group: Refinement description
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: [L-Ala51;Gly51']HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6772
Polymers21,9061
Non-polymers7711
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.695, 58.074, 61.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein [L-Ala51;Gly51']HIV-1 protease


Mass: 21905.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P03369*PLUS, HIV-1 retropepsin
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M CITRATE, 0.2 M SODIUM PHOSPHATE, 30% (V/V) AMMONIUM SULFATE, 10% (V/V) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2007
Details: BENT CONICAL SI-MIRROR (RH COATING); BENT GE(111) MONOCHROMATOR
RadiationMonochromator: BENT GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 36259 / % possible obs: 98.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 25.46
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.85 / Num. unique all: 3370 / % possible all: 93

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPv.5phasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Molrep v.5
Starting model: 3HAU

3hau


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.619 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21728 1805 5 %RANDOM
Rwork0.19649 ---
obs0.19751 34308 97.71 %-
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: 25.362 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2---0.63 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 54 137 1735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221722
X-RAY DIFFRACTIONr_bond_other_d0.0010.021153
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9932315
X-RAY DIFFRACTIONr_angle_other_deg0.9432837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61924.75461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54515300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8521510
X-RAY DIFFRACTIONr_chiral_restr0.1060.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02295
X-RAY DIFFRACTIONr_nbd_refined0.2210.2241
X-RAY DIFFRACTIONr_nbd_other0.2030.21111
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2784
X-RAY DIFFRACTIONr_nbtor_other0.0910.2912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3990.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2521.51131
X-RAY DIFFRACTIONr_mcbond_other0.3341.5464
X-RAY DIFFRACTIONr_mcangle_it1.88421762
X-RAY DIFFRACTIONr_scbond_it2.7263665
X-RAY DIFFRACTIONr_scangle_it4.1044.5553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.403→1.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 109 -
Rwork0.232 2223 -
obs--85.96 %
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)
10.9832-0.14060.35061.33550.42770.89530.03630.0777-0.0334-0.00730.0152-0.01850.04890.082-0.0515-0.08620.0052-0.0067-0.06970.0061-0.07215.17471.164318.3086
25.8827-5.96325.052311.7827-3.55534.76670.22970.19550.077-0.4755-0.308-0.12670.20450.21810.07840.12520.0090.02690.1605-0.01640.13265.0897-1.447812.7591
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 203
2X-RAY DIFFRACTION2A204

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