data_6BEN # _entry.id 6BEN # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.397 _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 6BEN pdb_00006ben 10.2210/pdb6ben/pdb WWPDB D_1000230763 ? ? BMRB 30357 ? 10.13018/BMR30357 # 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 2017-12-27 2 'Structure model' 1 1 2020-01-01 3 'Structure model' 1 2 2023-06-14 4 'Structure model' 1 3 2024-10-30 # _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' 'Author supporting evidence' 2 2 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' Other 6 4 'Structure model' 'Data collection' 7 4 'Structure model' 'Database references' 8 4 'Structure model' 'Structure summary' # 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' pdbx_audit_support 2 2 'Structure model' pdbx_nmr_software 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_database_status 5 3 'Structure model' struct_conn 6 4 'Structure model' chem_comp_atom 7 4 'Structure model' chem_comp_bond 8 4 'Structure model' database_2 9 4 'Structure model' pdbx_entry_details 10 4 'Structure model' pdbx_modification_feature # 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' '_pdbx_audit_support.funding_organization' 2 2 'Structure model' '_pdbx_nmr_software.name' 3 3 'Structure model' '_database_2.pdbx_DOI' 4 3 'Structure model' '_database_2.pdbx_database_accession' 5 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' 6 3 'Structure model' '_struct_conn.pdbx_dist_value' 7 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 8 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 9 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 10 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 11 4 'Structure model' '_database_2.pdbx_DOI' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 6BEN _pdbx_database_status.recvd_initial_deposition_date 2017-10-25 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'Solution structure of de novo macrocycle design8.2' _pdbx_database_related.db_id 30357 _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Shortridge, M.D.' 1 0000-0003-2825-6836 'Hosseinzadeh, P.' 2 ? 'Pardo-Avila, F.' 3 ? 'Varani, G.' 4 ? 'Baker, B.' 5 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Science _citation.journal_id_ASTM SCIEAS _citation.journal_id_CSD 0038 _citation.journal_id_ISSN 1095-9203 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 358 _citation.language ? _citation.page_first 1461 _citation.page_last 1466 _citation.title 'Comprehensive computational design of ordered peptide macrocycles.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1126/science.aap7577 _citation.pdbx_database_id_PubMed 29242347 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hosseinzadeh, P.' 1 ? primary 'Bhardwaj, G.' 2 ? primary 'Mulligan, V.K.' 3 ? primary 'Shortridge, M.D.' 4 ? primary 'Craven, T.W.' 5 ? primary 'Pardo-Avila, F.' 6 ? primary 'Rettie, S.A.' 7 ? primary 'Kim, D.E.' 8 ? primary 'Silva, D.A.' 9 ? primary 'Ibrahim, Y.M.' 10 ? primary 'Webb, I.K.' 11 ? primary 'Cort, J.R.' 12 ? primary 'Adkins, J.N.' 13 ? primary 'Varani, G.' 14 ? primary 'Baker, D.' 15 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description '(DAR)Q(DPR)(DGN)R(DGL)PQ' _entity.formula_weight 1040.133 _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 yes _entity_poly.pdbx_seq_one_letter_code '(DAR)Q(DPR)(DGN)R(DGL)PQ' _entity_poly.pdbx_seq_one_letter_code_can RQPQREPQ _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 DAR n 1 2 GLN n 1 3 DPR n 1 4 DGN n 1 5 ARG n 1 6 DGL n 1 7 PRO n 1 8 GLN 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 8 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # 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 DAR 'D-peptide linking' . D-ARGININE ? 'C6 H15 N4 O2 1' 175.209 DGL 'D-peptide linking' . 'D-GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 DGN 'D-peptide linking' . D-GLUTAMINE ? 'C5 H10 N2 O3' 146.144 DPR 'D-peptide linking' . D-PROLINE ? 'C5 H9 N O2' 115.130 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 # 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 DAR 1 1 1 DAR DAR A . n A 1 2 GLN 2 2 2 GLN GLN A . n A 1 3 DPR 3 3 3 DPR DPR A . n A 1 4 DGN 4 4 4 DGN DGN A . n A 1 5 ARG 5 5 5 ARG ARG A . n A 1 6 DGL 6 6 6 DGL DGU A . n A 1 7 PRO 7 7 7 PRO PRO A . n A 1 8 GLN 8 8 8 GLN GLN A . n # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 6BEN _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6BEN _struct.title 'Solution structure of de novo macrocycle design8.2' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6BEN _struct_keywords.text 'macrocycle, de novo, DE NOVO PROTEIN' _struct_keywords.pdbx_keywords 'DE NOVO 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_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6BEN _struct_ref.pdbx_db_accession 6BEN _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 6BEN _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 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6BEN _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _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 8 # _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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 1040 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _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 ? _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_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DAR 1 C ? ? ? 1_555 A GLN 2 N ? ? A DAR 1 A GLN 2 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale2 covale both ? A DAR 1 N ? ? ? 1_555 A GLN 8 C ? ? A DAR 1 A GLN 8 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale3 covale both ? A GLN 2 C ? ? ? 1_555 A DPR 3 N ? ? A GLN 2 A DPR 3 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale4 covale both ? A DPR 3 C ? ? ? 1_555 A DGN 4 N ? ? A DPR 3 A DGN 4 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale5 covale both ? A DGN 4 C ? ? ? 1_555 A ARG 5 N ? ? A DGN 4 A ARG 5 1_555 ? ? ? ? ? ? ? 1.336 ? ? covale6 covale both ? A ARG 5 C ? ? ? 1_555 A DGL 6 N ? ? A ARG 5 A DGL 6 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale7 covale both ? A DGL 6 C ? ? ? 1_555 A PRO 7 N ? ? A DGL 6 A PRO 7 1_555 ? ? ? ? ? ? ? 1.330 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_modification_feature.ordinal 1 _pdbx_modification_feature.label_comp_id DAR _pdbx_modification_feature.label_asym_id A _pdbx_modification_feature.label_seq_id 1 _pdbx_modification_feature.label_alt_id ? _pdbx_modification_feature.modified_residue_label_comp_id GLN _pdbx_modification_feature.modified_residue_label_asym_id A _pdbx_modification_feature.modified_residue_label_seq_id 8 _pdbx_modification_feature.modified_residue_label_alt_id ? _pdbx_modification_feature.auth_comp_id DAR _pdbx_modification_feature.auth_asym_id A _pdbx_modification_feature.auth_seq_id 1 _pdbx_modification_feature.PDB_ins_code ? _pdbx_modification_feature.symmetry 1_555 _pdbx_modification_feature.modified_residue_auth_comp_id GLN _pdbx_modification_feature.modified_residue_auth_asym_id A _pdbx_modification_feature.modified_residue_auth_seq_id 8 _pdbx_modification_feature.modified_residue_PDB_ins_code ? _pdbx_modification_feature.modified_residue_symmetry 1_555 _pdbx_modification_feature.comp_id_linking_atom N _pdbx_modification_feature.modified_residue_id_linking_atom C _pdbx_modification_feature.modified_residue_id . _pdbx_modification_feature.ref_pcm_id . _pdbx_modification_feature.ref_comp_id . _pdbx_modification_feature.type None _pdbx_modification_feature.category 'Non-standard linkage' # _pdbx_entry_details.entry_id 6BEN _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification Y # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 4 N A DAR 1 ? ? O A GLN 8 ? ? 2.17 2 6 N A DAR 1 ? ? O A GLN 8 ? ? 2.17 3 12 N A DAR 1 ? ? O A GLN 8 ? ? 2.15 4 15 N A DAR 1 ? ? O A GLN 8 ? ? 2.19 5 17 N A DAR 1 ? ? O A GLN 8 ? ? 2.18 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH1 A DAR 1 ? ? 116.04 120.30 -4.26 0.50 N 2 1 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 124.60 120.30 4.30 0.50 N 3 2 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH1 A DAR 1 ? ? 125.61 120.30 5.31 0.50 N 4 3 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH2 A DAR 1 ? ? 127.12 120.30 6.82 0.50 N 5 3 C A GLN 2 ? ? N A DPR 3 ? ? CA A DPR 3 ? ? 128.56 119.30 9.26 1.50 Y 6 3 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 126.15 120.30 5.85 0.50 N 7 4 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH1 A ARG 5 ? ? 123.62 120.30 3.32 0.50 N 8 5 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH1 A DAR 1 ? ? 114.50 120.30 -5.80 0.50 N 9 5 OE1 A DGL 6 ? ? CD A DGL 6 ? ? OE2 A DGL 6 ? ? 114.07 123.30 -9.23 1.20 N 10 6 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH2 A DAR 1 ? ? 126.04 120.30 5.74 0.50 N 11 6 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH1 A ARG 5 ? ? 114.47 120.30 -5.83 0.50 N 12 6 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 126.12 120.30 5.82 0.50 N 13 6 OE1 A DGL 6 ? ? CD A DGL 6 ? ? OE2 A DGL 6 ? ? 115.37 123.30 -7.93 1.20 N 14 7 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH1 A DAR 1 ? ? 116.92 120.30 -3.38 0.50 N 15 7 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH2 A DAR 1 ? ? 125.40 120.30 5.10 0.50 N 16 7 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH1 A ARG 5 ? ? 123.71 120.30 3.41 0.50 N 17 7 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 123.31 120.30 3.01 0.50 N 18 8 CD A DAR 1 ? ? NE A DAR 1 ? ? CZ A DAR 1 ? ? 133.05 123.60 9.45 1.40 N 19 8 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH1 A ARG 5 ? ? 112.22 120.30 -8.08 0.50 N 20 8 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 125.42 120.30 5.12 0.50 N 21 9 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH1 A ARG 5 ? ? 116.74 120.30 -3.56 0.50 N 22 9 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 125.34 120.30 5.04 0.50 N 23 10 NH1 A DAR 1 ? ? CZ A DAR 1 ? ? NH2 A DAR 1 ? ? 112.67 119.40 -6.73 1.10 N 24 10 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH1 A DAR 1 ? ? 117.11 120.30 -3.19 0.50 N 25 10 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH2 A DAR 1 ? ? 130.21 120.30 9.91 0.50 N 26 10 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 123.35 120.30 3.05 0.50 N 27 14 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH1 A ARG 5 ? ? 123.60 120.30 3.30 0.50 N 28 15 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH2 A DAR 1 ? ? 123.92 120.30 3.62 0.50 N 29 15 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 126.17 120.30 5.87 0.50 N 30 16 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH1 A DAR 1 ? ? 116.31 120.30 -3.99 0.50 N 31 17 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH1 A DAR 1 ? ? 116.31 120.30 -3.99 0.50 N 32 17 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH2 A DAR 1 ? ? 124.90 120.30 4.60 0.50 N 33 17 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH1 A ARG 5 ? ? 123.32 120.30 3.02 0.50 N 34 18 NH1 A DAR 1 ? ? CZ A DAR 1 ? ? NH2 A DAR 1 ? ? 106.74 119.40 -12.66 1.10 N 35 18 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH1 A DAR 1 ? ? 128.09 120.30 7.79 0.50 N 36 18 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH2 A DAR 1 ? ? 125.02 120.30 4.72 0.50 N 37 18 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 126.00 120.30 5.70 0.50 N 38 19 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH1 A DAR 1 ? ? 117.15 120.30 -3.15 0.50 N 39 19 NH1 A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 112.08 119.40 -7.32 1.10 N 40 19 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH2 A ARG 5 ? ? 126.42 120.30 6.12 0.50 N 41 19 N A PRO 7 ? ? CD A PRO 7 ? ? CG A PRO 7 ? ? 112.70 103.20 9.50 1.50 N 42 20 NE A DAR 1 ? ? CZ A DAR 1 ? ? NH2 A DAR 1 ? ? 126.25 120.30 5.95 0.50 N # 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 3 PRO A 7 ? ? -49.26 -16.61 2 5 ARG A 5 ? ? -114.53 70.92 3 5 DGL A 6 ? ? -37.06 -58.31 4 6 DGL A 6 ? ? -44.42 -73.41 5 9 DGL A 6 ? ? -38.68 -49.97 6 13 DGL A 6 ? ? -38.98 -56.44 7 15 DGL A 6 ? ? -36.51 -56.33 8 18 DGL A 6 ? ? -37.41 -75.60 # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 16 _pdbx_validate_peptide_omega.auth_comp_id_1 GLN _pdbx_validate_peptide_omega.auth_asym_id_1 A _pdbx_validate_peptide_omega.auth_seq_id_1 2 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 ? _pdbx_validate_peptide_omega.auth_comp_id_2 DPR _pdbx_validate_peptide_omega.auth_asym_id_2 A _pdbx_validate_peptide_omega.auth_seq_id_2 3 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 ? _pdbx_validate_peptide_omega.omega 136.71 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 4 ARG A 5 ? ? 0.116 'SIDE CHAIN' 2 9 ARG A 5 ? ? 0.089 'SIDE CHAIN' # _pdbx_nmr_ensemble.entry_id 6BEN _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _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 6BEN _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '5 mg/mL Design8.2, 5 % [U-2H] glycerol, 90% H2O/10% D2O' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' _pdbx_nmr_sample_details.label dsh_1 _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details ? # loop_ _pdbx_nmr_exptl_sample.solution_id _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 1 Design8.2 5 ? mg/mL 'natural abundance' 1 glycerol 5 ? % '[U-2H]' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 278 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 5.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0 _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units 'Not defined' _pdbx_nmr_exptl_sample_conditions.label conditions_1 _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '2D 1H-1H TOCSY' 1 isotropic 2 1 1 '2D 1H-1H NOESY' 1 isotropic 3 1 1 '2D 1H-15N HSQC' 1 isotropic # _pdbx_nmr_refine.entry_id 6BEN _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 refinement GROMACS 2016.1 Abraham 2 'structure calculation' 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 3 'chemical shift assignment' Sparky ? Goddard 4 'peak picking' Sparky ? Goddard # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ARG N N N N 1 ARG CA C N S 2 ARG C C N N 3 ARG O O N N 4 ARG CB C N N 5 ARG CG C N N 6 ARG CD C N N 7 ARG NE N N N 8 ARG CZ C N N 9 ARG NH1 N N N 10 ARG NH2 N N N 11 ARG OXT O N N 12 ARG H H N N 13 ARG H2 H N N 14 ARG HA H N N 15 ARG HB2 H N N 16 ARG HB3 H N N 17 ARG HG2 H N N 18 ARG HG3 H N N 19 ARG HD2 H N N 20 ARG HD3 H N N 21 ARG HE H N N 22 ARG HH11 H N N 23 ARG HH12 H N N 24 ARG HH21 H N N 25 ARG HH22 H N N 26 ARG HXT H N N 27 DAR N N N N 28 DAR CA C N R 29 DAR CB C N N 30 DAR CG C N N 31 DAR CD C N N 32 DAR NE N N N 33 DAR CZ C N N 34 DAR NH1 N N N 35 DAR NH2 N N N 36 DAR C C N N 37 DAR O O N N 38 DAR OXT O N N 39 DAR H H N N 40 DAR H2 H N N 41 DAR HA H N N 42 DAR HB2 H N N 43 DAR HB3 H N N 44 DAR HG2 H N N 45 DAR HG3 H N N 46 DAR HD2 H N N 47 DAR HD3 H N N 48 DAR HE H N N 49 DAR HH11 H N N 50 DAR HH12 H N N 51 DAR HH21 H N N 52 DAR HH22 H N N 53 DAR HXT H N N 54 DGL N N N N 55 DGL CA C N R 56 DGL C C N N 57 DGL O O N N 58 DGL CB C N N 59 DGL CG C N N 60 DGL CD C N N 61 DGL OE1 O N N 62 DGL OE2 O N N 63 DGL OXT O N N 64 DGL H H N N 65 DGL H2 H N N 66 DGL HA H N N 67 DGL HB2 H N N 68 DGL HB3 H N N 69 DGL HG2 H N N 70 DGL HG3 H N N 71 DGL HE2 H N N 72 DGL HXT H N N 73 DGN N N N N 74 DGN CA C N R 75 DGN C C N N 76 DGN O O N N 77 DGN OXT O N N 78 DGN CB C N N 79 DGN CG C N N 80 DGN CD C N N 81 DGN OE1 O N N 82 DGN NE2 N N N 83 DGN H H N N 84 DGN H2 H N N 85 DGN HA H N N 86 DGN HXT H N N 87 DGN HB2 H N N 88 DGN HB3 H N N 89 DGN HG2 H N N 90 DGN HG3 H N N 91 DGN HE21 H N N 92 DGN HE22 H N N 93 DPR N N N N 94 DPR CA C N R 95 DPR CB C N N 96 DPR CG C N N 97 DPR CD C N N 98 DPR C C N N 99 DPR O O N N 100 DPR OXT O N N 101 DPR H H N N 102 DPR HA H N N 103 DPR HB2 H N N 104 DPR HB3 H N N 105 DPR HG2 H N N 106 DPR HG3 H N N 107 DPR HD2 H N N 108 DPR HD3 H N N 109 DPR HXT H N N 110 GLN N N N N 111 GLN CA C N S 112 GLN C C N N 113 GLN O O N N 114 GLN CB C N N 115 GLN CG C N N 116 GLN CD C N N 117 GLN OE1 O N N 118 GLN NE2 N N N 119 GLN OXT O N N 120 GLN H H N N 121 GLN H2 H N N 122 GLN HA H N N 123 GLN HB2 H N N 124 GLN HB3 H N N 125 GLN HG2 H N N 126 GLN HG3 H N N 127 GLN HE21 H N N 128 GLN HE22 H N N 129 GLN HXT H N N 130 PRO N N N N 131 PRO CA C N S 132 PRO C C N N 133 PRO O O N N 134 PRO CB C N N 135 PRO CG C N N 136 PRO CD C N N 137 PRO OXT O N N 138 PRO H H N N 139 PRO HA H N N 140 PRO HB2 H N N 141 PRO HB3 H N N 142 PRO HG2 H N N 143 PRO HG3 H N N 144 PRO HD2 H N N 145 PRO HD3 H N N 146 PRO HXT H N N 147 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ARG N CA sing N N 1 ARG N H sing N N 2 ARG N H2 sing N N 3 ARG CA C sing N N 4 ARG CA CB sing N N 5 ARG CA HA sing N N 6 ARG C O doub N N 7 ARG C OXT sing N N 8 ARG CB CG sing N N 9 ARG CB HB2 sing N N 10 ARG CB HB3 sing N N 11 ARG CG CD sing N N 12 ARG CG HG2 sing N N 13 ARG CG HG3 sing N N 14 ARG CD NE sing N N 15 ARG CD HD2 sing N N 16 ARG CD HD3 sing N N 17 ARG NE CZ sing N N 18 ARG NE HE sing N N 19 ARG CZ NH1 sing N N 20 ARG CZ NH2 doub N N 21 ARG NH1 HH11 sing N N 22 ARG NH1 HH12 sing N N 23 ARG NH2 HH21 sing N N 24 ARG NH2 HH22 sing N N 25 ARG OXT HXT sing N N 26 DAR N CA sing N N 27 DAR N H sing N N 28 DAR N H2 sing N N 29 DAR CA CB sing N N 30 DAR CA C sing N N 31 DAR CA HA sing N N 32 DAR CB CG sing N N 33 DAR CB HB2 sing N N 34 DAR CB HB3 sing N N 35 DAR CG CD sing N N 36 DAR CG HG2 sing N N 37 DAR CG HG3 sing N N 38 DAR CD NE sing N N 39 DAR CD HD2 sing N N 40 DAR CD HD3 sing N N 41 DAR NE CZ sing N N 42 DAR NE HE sing N N 43 DAR CZ NH1 sing N N 44 DAR CZ NH2 doub N N 45 DAR NH1 HH11 sing N N 46 DAR NH1 HH12 sing N N 47 DAR NH2 HH21 sing N N 48 DAR NH2 HH22 sing N N 49 DAR C O doub N N 50 DAR C OXT sing N N 51 DAR OXT HXT sing N N 52 DGL N CA sing N N 53 DGL N H sing N N 54 DGL N H2 sing N N 55 DGL CA C sing N N 56 DGL CA CB sing N N 57 DGL CA HA sing N N 58 DGL C O doub N N 59 DGL C OXT sing N N 60 DGL CB CG sing N N 61 DGL CB HB2 sing N N 62 DGL CB HB3 sing N N 63 DGL CG CD sing N N 64 DGL CG HG2 sing N N 65 DGL CG HG3 sing N N 66 DGL CD OE1 doub N N 67 DGL CD OE2 sing N N 68 DGL OE2 HE2 sing N N 69 DGL OXT HXT sing N N 70 DGN N CA sing N N 71 DGN N H sing N N 72 DGN N H2 sing N N 73 DGN CA C sing N N 74 DGN CA CB sing N N 75 DGN CA HA sing N N 76 DGN C O doub N N 77 DGN C OXT sing N N 78 DGN OXT HXT sing N N 79 DGN CB CG sing N N 80 DGN CB HB2 sing N N 81 DGN CB HB3 sing N N 82 DGN CG CD sing N N 83 DGN CG HG2 sing N N 84 DGN CG HG3 sing N N 85 DGN CD OE1 doub N N 86 DGN CD NE2 sing N N 87 DGN NE2 HE21 sing N N 88 DGN NE2 HE22 sing N N 89 DPR N CA sing N N 90 DPR N CD sing N N 91 DPR N H sing N N 92 DPR CA CB sing N N 93 DPR CA C sing N N 94 DPR CA HA sing N N 95 DPR CB CG sing N N 96 DPR CB HB2 sing N N 97 DPR CB HB3 sing N N 98 DPR CG CD sing N N 99 DPR CG HG2 sing N N 100 DPR CG HG3 sing N N 101 DPR CD HD2 sing N N 102 DPR CD HD3 sing N N 103 DPR C O doub N N 104 DPR C OXT sing N N 105 DPR OXT HXT sing N N 106 GLN N CA sing N N 107 GLN N H sing N N 108 GLN N H2 sing N N 109 GLN CA C sing N N 110 GLN CA CB sing N N 111 GLN CA HA sing N N 112 GLN C O doub N N 113 GLN C OXT sing N N 114 GLN CB CG sing N N 115 GLN CB HB2 sing N N 116 GLN CB HB3 sing N N 117 GLN CG CD sing N N 118 GLN CG HG2 sing N N 119 GLN CG HG3 sing N N 120 GLN CD OE1 doub N N 121 GLN CD NE2 sing N N 122 GLN NE2 HE21 sing N N 123 GLN NE2 HE22 sing N N 124 GLN OXT HXT sing N N 125 PRO N CA sing N N 126 PRO N CD sing N N 127 PRO N H sing N N 128 PRO CA C sing N N 129 PRO CA CB sing N N 130 PRO CA HA sing N N 131 PRO C O doub N N 132 PRO C OXT sing N N 133 PRO CB CG sing N N 134 PRO CB HB2 sing N N 135 PRO CB HB3 sing N N 136 PRO CG CD sing N N 137 PRO CG HG2 sing N N 138 PRO CG HG3 sing N N 139 PRO CD HD2 sing N N 140 PRO CD HD3 sing N N 141 PRO OXT HXT sing N N 142 # _pdbx_audit_support.funding_organization 'Department of Health & Human Services (HHS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 5R01GM103834 _pdbx_audit_support.ordinal 1 # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model DRX _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.details ? # _atom_sites.entry_id 6BEN _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 # loop_ #