data_1OMQ # _entry.id 1OMQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1OMQ pdb_00001omq 10.2210/pdb1omq/pdb RCSB RCSB018449 ? ? WWPDB D_1000018449 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1OMQ _pdbx_database_status.recvd_initial_deposition_date 2003-02-26 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Lindberg, M.' 1 'Biverstahl, H.' 2 'Graslund, A.' 3 'Maler, L.' 4 # _citation.id primary _citation.title 'Structure and positioning comparison of two variants of penetratin in two different membrane mimicking systems by NMR' _citation.journal_abbrev Eur.J.Biochem. _citation.journal_volume 270 _citation.page_first 3055 _citation.page_last 3063 _citation.year 2003 _citation.journal_id_ASTM EJBCAI _citation.country IX _citation.journal_id_ISSN 0014-2956 _citation.journal_id_CSD 0262 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12846839 _citation.pdbx_database_id_DOI 10.1046/j.1432-1033.2003.03685.x # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lindberg, M.' 1 ? primary 'Biverstahl, H.' 2 ? primary 'Graslund, A.' 3 ? primary 'Maler, L.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Homeotic antennapedia protein' _entity.formula_weight 2253.781 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'C-terminal fragment' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name penetratin # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code RQIKIWFQNRRMKWKK _entity_poly.pdbx_seq_one_letter_code_can RQIKIWFQNRRMKWKK _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ARG n 1 2 GLN n 1 3 ILE n 1 4 LYS n 1 5 ILE n 1 6 TRP n 1 7 PHE n 1 8 GLN n 1 9 ASN n 1 10 ARG n 1 11 ARG n 1 12 MET n 1 13 LYS n 1 14 TRP n 1 15 LYS n 1 16 LYS n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details ;THE Peptide WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE Peptide IS NATURALLY FOUND IN DROSOPHILA MELANOGASTER (fruit fly). The peptide was obtained from Neosystem Inc. and used without further purification. ; # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code ANTP_DROME _struct_ref.pdbx_db_accession P02833 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code RQIKIWFQNRRMKWKK _struct_ref.pdbx_align_begin 50 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1OMQ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 16 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P02833 _struct_ref_seq.db_align_beg 339 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 354 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 43 _struct_ref_seq.pdbx_auth_seq_align_end 58 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 '2D TOCSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 310 _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 5.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength '50mM KCl' _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '3mM penetratin, 50 mM KCl; 15% w/v (DMPC+DMPG)/DHPC bicellar solution with q=0.5 and 5% D2O' _pdbx_nmr_sample_details.solvent_system '15% w/v (DMPC+DMPG)/DHPC bicellar solution with q=0.5 and 5% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model UNITY _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 1OMQ _pdbx_nmr_refine.method 'distance geometry' _pdbx_nmr_refine.details ;A total of 129 distance constraints where identified, mostly sequential and medium range NOEs (40 intra-residue, 54 sequential and 35 medium range NOEs) ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1OMQ _pdbx_nmr_details.text 'Structure was determined by standard 2D homonuclear techniques' # _pdbx_nmr_ensemble.entry_id 1OMQ _pdbx_nmr_ensemble.conformers_calculated_total_number 60 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 1OMQ _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average,lowest energy' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal VNMR 6.1c collection ? 1 Felix 2000.1 'data analysis' ? 2 DYANA 1.5 'structure solution' 'Guntert, Mumenthaler, Herrmann' 3 DYANA 1.5 refinement 'Guntert, Mumenthaler, Herrmann' 4 # _exptl.entry_id 1OMQ _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1OMQ _struct.title 'Structure of penetratin in bicellar solution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1OMQ _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN' _struct_keywords.text 'unstructured at the terminals, alpha helical in the middle, DNA BINDING PROTEIN' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id TRP _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 6 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id LYS _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 15 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id TRP _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 48 _struct_conf.end_auth_comp_id LYS _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 57 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 10 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _database_PDB_matrix.entry_id 1OMQ _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1OMQ _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 ARG 1 43 43 ARG ARG A . n A 1 2 GLN 2 44 44 GLN GLN A . n A 1 3 ILE 3 45 45 ILE ILE A . n A 1 4 LYS 4 46 46 LYS LYS A . n A 1 5 ILE 5 47 47 ILE ILE A . n A 1 6 TRP 6 48 48 TRP TRP A . n A 1 7 PHE 7 49 49 PHE PHE A . n A 1 8 GLN 8 50 50 GLN GLN A . n A 1 9 ASN 9 51 51 ASN ASN A . n A 1 10 ARG 10 52 52 ARG ARG A . n A 1 11 ARG 11 53 53 ARG ARG A . n A 1 12 MET 12 54 54 MET MET A . n A 1 13 LYS 13 55 55 LYS LYS A . n A 1 14 TRP 14 56 56 TRP TRP A . n A 1 15 LYS 15 57 57 LYS LYS A . n A 1 16 LYS 16 58 58 LYS LYS A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2003-07-29 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 ILE _pdbx_validate_close_contact.auth_seq_id_1 47 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 HD21 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 ASN _pdbx_validate_close_contact.auth_seq_id_2 51 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.59 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 LYS A 57 ? ? -40.69 107.81 2 2 GLN A 44 ? ? -149.94 24.42 3 3 TRP A 56 ? ? -104.31 71.74 4 4 ARG A 53 ? ? -115.00 68.36 5 4 MET A 54 ? ? 161.05 -26.36 6 4 TRP A 56 ? ? -114.59 66.43 7 5 GLN A 44 ? ? 39.26 37.27 8 5 MET A 54 ? ? 38.71 58.23 9 8 ARG A 53 ? ? -92.11 57.63 10 8 MET A 54 ? ? 161.00 -26.27 11 9 GLN A 44 ? ? -96.74 34.01 12 10 LYS A 57 ? ? -46.37 109.95 13 11 GLN A 44 ? ? 174.59 -34.05 14 11 LYS A 55 ? ? -119.54 56.12 15 11 TRP A 56 ? ? -162.43 -47.13 16 12 GLN A 44 ? ? -148.22 19.28 17 12 MET A 54 ? ? -144.09 -44.59 18 12 LYS A 57 ? ? 47.61 -162.39 19 13 GLN A 44 ? ? -150.45 20.78 20 13 LYS A 55 ? ? -157.05 -45.84 21 14 GLN A 44 ? ? -147.06 19.77 22 14 TRP A 56 ? ? -133.00 -49.01 23 15 GLN A 44 ? ? -156.40 28.40 24 15 ARG A 53 ? ? -105.84 63.92 25 15 MET A 54 ? ? 165.47 -28.82 26 15 LYS A 57 ? ? 179.54 -179.83 27 16 LYS A 57 ? ? 70.60 -75.79 28 17 GLN A 44 ? ? 39.90 29.30 29 17 LYS A 57 ? ? 64.37 119.29 30 18 LYS A 57 ? ? 64.98 170.20 31 19 GLN A 44 ? ? -147.62 -149.65 32 19 ILE A 45 ? ? 39.95 31.38 33 19 LYS A 46 ? ? -164.04 -39.10 34 20 GLN A 44 ? ? 86.42 -13.66 #