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- PDB-3fsm: CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED 203 AMINO ACID 'COV... -

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Basic information

Entry
Database: PDB / ID: 3fsm
TitleCRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED 203 AMINO ACID 'COVALENT DIMER' [L-Ala51,D-Ala51'] HIV-1 PROTEASE MOLECULE
ComponentsCOVALENT DIMER [L-Ala51, D-Ala51'] HIV-1 PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / asymmetric dimer / covalent dimer / beta-sheet / 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 / viral genome integration into host DNA / RNA-directed DNA polymerase / 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 / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / 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. / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / 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 / Resolution: 1.6 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
DepositionJan 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary / Version format compliance
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
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_sheet / 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_sheet.number_strands / _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
Revision 1.7Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COVALENT DIMER [L-Ala51, D-Ala51'] HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6912
Polymers21,9201
Non-polymers7711
Water2,126118
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.472, 58.286, 61.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein COVALENT DIMER [L-Ala51, D-Ala51'] HIV-1 PROTEASE


Mass: 21919.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Total chemical protein synthesis / 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 / Details: Total chemical peptide synthesis
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.: 118 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M CITRATE, 0.2M SODIUM PHOPHATE, 30% (W/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: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2007
Details: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing with two additional horizontally deflecting mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 25109 / Num. obs: 25109 / % possible obs: 99.8 % / Observed criterion σ(I): 81.1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.079 / Χ2: 1.53 / Net I/σ(I): 22.636
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2419 / Χ2: 1.58 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MOLREPphasing
RefinementStarting model: PDB ENTRY 2O40

2o40


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.804 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1274 5.1 %RANDOM
Rwork0.199 ---
obs0.201 25039 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.86 Å2 / Biso mean: 25.825 Å2 / Biso min: 13.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 54 118 1717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221629
X-RAY DIFFRACTIONr_bond_other_d0.0010.021098
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.992203
X-RAY DIFFRACTIONr_angle_other_deg0.90132705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4125204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.54124.91559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68115288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.876159
X-RAY DIFFRACTIONr_chiral_restr0.1110.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
X-RAY DIFFRACTIONr_nbd_refined0.1920.2217
X-RAY DIFFRACTIONr_nbd_other0.1950.21051
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2767
X-RAY DIFFRACTIONr_nbtor_other0.0880.2874
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.010.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.26
X-RAY DIFFRACTIONr_mcbond_it1.0811.51062
X-RAY DIFFRACTIONr_mcbond_other0.321.5431
X-RAY DIFFRACTIONr_mcangle_it1.61721674
X-RAY DIFFRACTIONr_scbond_it2.4493638
X-RAY DIFFRACTIONr_scangle_it3.6944.5529
LS refinement shellResolution: 1.598→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 102 -
Rwork0.265 1654 -
all-1756 -
obs-1654 97.5 %
Refinement TLS params.Method: refined / Origin x: 5.089 Å / Origin y: 1.181 Å / Origin z: 18.214 Å
111213212223313233
T-0.116 Å2-0.0017 Å2-0.0033 Å2--0.1238 Å20.0088 Å2---0.1663 Å2
L2.3501 °2-0.8509 °20.4832 °2-2.0535 °20.6234 °2--1.306 °2
S0.0241 Å °0.0982 Å °-0.0555 Å °0.0313 Å °0.0558 Å °-0.0424 Å °0.035 Å °0.1324 Å °-0.0799 Å °

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