data_2ND8 # _entry.id 2ND8 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_code _database_2.database_id _database_2.pdbx_database_accession _database_2.pdbx_DOI RCSB104718 RCSB ? ? 2ND8 PDB pdb_00002nd8 10.2210/pdb2nd8/pdb 26051 BMRB ? ? D_1000104718 WWPDB ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 26051 BMRB unspecified . 2ND6 PDB unspecified . 2ND7 PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2ND8 _pdbx_database_status.methods_development_category ? _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2016-05-11 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Bera, S.' 1 'Bhunia, A.' 2 # _citation.id primary _citation.title ;Structural Elucidation of the Cell-Penetrating Penetratin Peptide in Model Membranes at the Atomic Level: Probing Hydrophobic Interactions in the Blood-Brain Barrier ; _citation.journal_abbrev Biochemistry _citation.journal_volume 55 _citation.page_first 4982 _citation.page_last 4996 _citation.year 2016 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 27532224 _citation.pdbx_database_id_DOI 10.1021/acs.biochem.6b00518 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Bera, S.' 1 ? primary 'Kar, R.K.' 2 ? primary 'Mondal, S.' 3 ? primary 'Pahan, K.' 4 ? primary 'Bhunia, A.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Cell penetrating peptide' _entity.formula_weight 2368.869 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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 DRQIKIWFQNRRMKWKK _entity_poly.pdbx_seq_one_letter_code_can DRQIKIWFQNRRMKWKK _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 ASP n 1 2 ARG n 1 3 GLN n 1 4 ILE n 1 5 LYS n 1 6 ILE n 1 7 TRP n 1 8 PHE n 1 9 GLN n 1 10 ASN n 1 11 ARG n 1 12 ARG n 1 13 MET n 1 14 LYS n 1 15 TRP n 1 16 LYS n 1 17 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 'Drosophila melanogaster' _pdbx_entity_src_syn.organism_common_name 'Fruit fly' _pdbx_entity_src_syn.ncbi_taxonomy_id 7227 _pdbx_entity_src_syn.details ;Synthetic peptide, modified version of Penetratin peptide, derived from Antennapedia Homeodomain protein (3rd Helix) of Drosophila melanogaster ; # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2ND8 _struct_ref.pdbx_db_accession 2ND8 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2ND8 _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 17 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2ND8 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 17 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 17 # 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 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 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.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H TOCSY' 1 2 1 '2D 1H-1H NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 10 _pdbx_nmr_exptl_sample_conditions.pH 4.5 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 288 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '0.5 mM CELL PENETRATING PEPTIDES-1, 55.5 mM H2O-2, 50 mM D2O-3, 0.5 mM DSS-4, 90% H2O/10% D2O' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.field_strength 700 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2ND8 _pdbx_nmr_refine.method 'distance geometry' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2ND8 _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.representative_conformer 1 _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2ND8 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.ordinal _pdbx_nmr_software.version 'Guntert, Mumenthaler and Wuthrich' 'structure solution' CYANA 1 2.1 ? refinement CYANA 2 ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2ND8 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2ND8 _struct.title 'Structures of DK17 in TBLE LUVS' _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2ND8 _struct_keywords.pdbx_keywords 'LIPID BINDING PROTEIN' _struct_keywords.text 'LIPID 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_biol.details ? # _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 7 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ARG _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 12 _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 7 _struct_conf.end_auth_comp_id ARG _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 12 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 6 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 2ND8 _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 ASP 1 1 1 ASP ASP A . n A 1 2 ARG 2 2 2 ARG ARG A . n A 1 3 GLN 3 3 3 GLN GLN A . n A 1 4 ILE 4 4 4 ILE ILE A . n A 1 5 LYS 5 5 5 LYS LYS A . n A 1 6 ILE 6 6 6 ILE ILE A . n A 1 7 TRP 7 7 7 TRP TRP A . n A 1 8 PHE 8 8 8 PHE PHE A . n A 1 9 GLN 9 9 9 GLN GLN A . n A 1 10 ASN 10 10 10 ASN ASN A . n A 1 11 ARG 11 11 11 ARG ARG A . n A 1 12 ARG 12 12 12 ARG ARG A . n A 1 13 MET 13 13 13 MET MET A . n A 1 14 LYS 14 14 14 LYS LYS A . n A 1 15 TRP 15 15 15 TRP TRP A . n A 1 16 LYS 16 16 16 LYS LYS A . n A 1 17 LYS 17 17 17 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 2017-03-22 2 'Structure model' 1 1 2023-06-14 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' Other # 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 2 'Structure model' database_2 2 2 'Structure model' pdbx_database_status 3 2 'Structure model' pdbx_nmr_spectrometer # 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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 2 'Structure model' '_pdbx_nmr_spectrometer.model' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id 'CELL PENETRATING PEPTIDES-1' 0.5 ? mM ? 1 H2O-2 55.5 ? mM ? 1 D2O-3 50 ? mM ? 1 DSS-4 0.5 ? mM ? 1 # 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 ARG A 2 ? ? -120.13 -75.49 2 1 GLN A 3 ? ? -120.20 -75.31 3 1 ARG A 12 ? ? -113.06 51.48 4 1 MET A 13 ? ? -120.36 -76.23 5 2 ARG A 2 ? ? -120.04 -75.48 6 2 GLN A 3 ? ? -120.14 -74.81 7 2 MET A 13 ? ? -120.34 -76.26 8 3 ARG A 2 ? ? -120.08 -75.36 9 3 GLN A 3 ? ? -120.12 -74.75 10 3 LYS A 14 ? ? -81.52 41.98 11 4 ARG A 2 ? ? -120.10 -76.85 12 4 GLN A 3 ? ? -120.69 -75.85 13 4 MET A 13 ? ? -46.37 -76.68 14 5 ARG A 12 ? ? -114.71 53.57 15 5 MET A 13 ? ? -120.33 -76.31 16 6 GLN A 3 ? ? -60.90 -71.53 17 6 ARG A 12 ? ? -57.60 -74.91 18 7 GLN A 3 ? ? -67.36 -76.98 19 7 LYS A 5 ? ? -91.77 43.58 20 7 LYS A 14 ? ? -81.86 41.50 21 8 LYS A 5 ? ? -109.59 72.30 22 8 MET A 13 ? ? -120.38 -76.44 23 9 GLN A 3 ? ? -51.79 -74.71 24 9 LYS A 14 ? ? -81.06 43.28 25 10 ARG A 2 ? ? -106.50 -75.27 26 10 GLN A 3 ? ? -120.14 -74.71 27 10 ARG A 12 ? ? -57.17 -75.13 28 10 LYS A 14 ? ? -81.13 43.15 29 11 ARG A 12 ? ? -111.08 -75.05 30 12 LYS A 14 ? ? -81.71 41.84 31 13 ARG A 2 ? ? -120.77 -78.28 32 13 GLN A 3 ? ? -120.95 -69.84 33 13 LYS A 14 ? ? -81.04 43.26 34 14 MET A 13 ? ? -45.02 -75.80 35 15 MET A 13 ? ? -120.29 -76.37 36 16 MET A 13 ? ? -45.84 -75.97 37 17 LYS A 14 ? ? -81.64 41.87 38 18 ARG A 2 ? ? -121.12 -85.02 39 18 GLN A 3 ? ? -122.62 -77.94 40 18 ARG A 12 ? ? -51.06 -80.64 41 18 MET A 13 ? ? -121.56 -79.59 42 19 LYS A 14 ? ? -81.67 41.86 43 20 ARG A 2 ? ? -120.06 -75.11 44 20 GLN A 3 ? ? -120.14 -76.28 45 20 ILE A 4 ? ? -118.02 -78.58 46 20 LYS A 14 ? ? -81.07 43.25 #