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Basic information

Entry
Database: PDB / ID: 3ovn
TitleFragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase
ComponentsPOL polyprotein
KeywordsVIRAL PROTEIN/TRANSFERASE INHIBITOR / DNA INTEGRATION / AIDS / INTEGRASE / ENDONUCLEASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING / VIRAL PROTEIN / RNaseH / FRAGMENT BINDING / VIRAL PROTEIN-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / host cell / viral nucleocapsid / DNA recombination / aspartic-type endopeptidase activity / 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 / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / 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 ...Ribonuclease H-like superfamily/Ribonuclease H / 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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / : / 1-methyl-3-(thiophen-2-yl)-1H-pyrazol-5-amine / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWielens, J. / Chalmers, D.K. / Headey, S.J. / Deadman, J.J. / Rhodes, D.K. / Parker, M.W. / Scanlon, M.J.
CitationJournal: Chemmedchem / Year: 2011
Title: Fragment-based design of ligands targeting a novel site on the integrase enzyme of human immunodeficiency virus 1
Authors: Wielens, J. / Headey, S.J. / Deadman, J.J. / Rhodes, D.I. / Parker, M.W. / Chalmers, D.K. / Scanlon, M.J.
History
DepositionSep 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POL polyprotein
B: POL polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,94711
Polymers35,6042
Non-polymers1,3439
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-14 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.750, 59.704, 81.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein POL polyprotein


Mass: 17802.174 Da / Num. of mol.: 2 / Fragment: Integrase CATALYTIC CORE DOMAIN, 765-927 / Mutation: C56S, W131D, F139D, F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL43 / Gene: pol / Plasmid: PET23B+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q72498
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 65 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPV / 1-methyl-3-(thiophen-2-yl)-1H-pyrazol-5-amine


Mass: 179.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9N3S
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2007 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.25 Å / Num. all: 23203 / Num. obs: 21811 / % possible obs: 99.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 22.38 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.112 / Net I/σ(I): 9.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3184 / Rsym value: 0.479 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L3U

3l3u


Resolution: 1.95→40.91 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.656 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24882 1117 5.1 %RANDOM
Rwork0.21084 ---
obs0.21278 20602 98.83 %-
all-21811 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.036 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2--3.24 Å20 Å2
3----2.41 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 61 57 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222266
X-RAY DIFFRACTIONr_bond_other_d0.0010.021472
X-RAY DIFFRACTIONr_angle_refined_deg2.1741.9623073
X-RAY DIFFRACTIONr_angle_other_deg1.06233615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23125.05493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8615379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.879158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1891.51397
X-RAY DIFFRACTIONr_mcbond_other0.2771.5586
X-RAY DIFFRACTIONr_mcangle_it2.12422242
X-RAY DIFFRACTIONr_scbond_it2.8973869
X-RAY DIFFRACTIONr_scangle_it4.4724.5831
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 92 -
Rwork0.27 1517 -
obs--99.63 %

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