data_2DIR # _entry.id 2DIR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2DIR pdb_00002dir 10.2210/pdb2dir/pdb RCSB RCSB025460 ? ? WWPDB D_1000025460 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id hss001001550.1 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2DIR _pdbx_database_status.recvd_initial_deposition_date 2006-03-30 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _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 'Dang, W.' 1 'Muto, Y.' 2 'Inoue, M.' 3 'Kigawa, T.' 4 'Shirouzu, M.' 5 'Terada, T.' 6 'Yokoyama, S.' 7 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 8 # _citation.id primary _citation.title 'Solution structure of the THUMP domain of THUMP domain-containing protein 1' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dang, W.' 1 ? primary 'Muto, Y.' 2 ? primary 'Inoue, M.' 3 ? primary 'Kigawa, T.' 4 ? primary 'Shirouzu, M.' 5 ? primary 'Terada, T.' 6 ? primary 'Yokoyama, S.' 7 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'THUMP domain-containing protein 1' _entity.formula_weight 10755.237 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'THUMP domain' _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 ;GSSGSSGKAFLEDMKKYAETFLEPWFKAPNKGTFQIVYKSRNNSHVNREEVIRELAGIVCTLNSENKVDLTNPQYTVVVE IIKAVCCLSVVKSGPSSG ; _entity_poly.pdbx_seq_one_letter_code_can ;GSSGSSGKAFLEDMKKYAETFLEPWFKAPNKGTFQIVYKSRNNSHVNREEVIRELAGIVCTLNSENKVDLTNPQYTVVVE IIKAVCCLSVVKSGPSSG ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier hss001001550.1 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 SER n 1 3 SER n 1 4 GLY n 1 5 SER n 1 6 SER n 1 7 GLY n 1 8 LYS n 1 9 ALA n 1 10 PHE n 1 11 LEU n 1 12 GLU n 1 13 ASP n 1 14 MET n 1 15 LYS n 1 16 LYS n 1 17 TYR n 1 18 ALA n 1 19 GLU n 1 20 THR n 1 21 PHE n 1 22 LEU n 1 23 GLU n 1 24 PRO n 1 25 TRP n 1 26 PHE n 1 27 LYS n 1 28 ALA n 1 29 PRO n 1 30 ASN n 1 31 LYS n 1 32 GLY n 1 33 THR n 1 34 PHE n 1 35 GLN n 1 36 ILE n 1 37 VAL n 1 38 TYR n 1 39 LYS n 1 40 SER n 1 41 ARG n 1 42 ASN n 1 43 ASN n 1 44 SER n 1 45 HIS n 1 46 VAL n 1 47 ASN n 1 48 ARG n 1 49 GLU n 1 50 GLU n 1 51 VAL n 1 52 ILE n 1 53 ARG n 1 54 GLU n 1 55 LEU n 1 56 ALA n 1 57 GLY n 1 58 ILE n 1 59 VAL n 1 60 CYS n 1 61 THR n 1 62 LEU n 1 63 ASN n 1 64 SER n 1 65 GLU n 1 66 ASN n 1 67 LYS n 1 68 VAL n 1 69 ASP n 1 70 LEU n 1 71 THR n 1 72 ASN n 1 73 PRO n 1 74 GLN n 1 75 TYR n 1 76 THR n 1 77 VAL n 1 78 VAL n 1 79 VAL n 1 80 GLU n 1 81 ILE n 1 82 ILE n 1 83 LYS n 1 84 ALA n 1 85 VAL n 1 86 CYS n 1 87 CYS n 1 88 LEU n 1 89 SER n 1 90 VAL n 1 91 VAL n 1 92 LYS n 1 93 SER n 1 94 GLY n 1 95 PRO n 1 96 SER n 1 97 SER n 1 98 GLY n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus Homo _entity_src_gen.pdbx_gene_src_gene THUMPD1 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Cell free synthesis' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ? _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type PLASMID _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name P050905-19 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description 'Cell free protein synthesis' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code THUM1_HUMAN _struct_ref.pdbx_db_accession Q9NXG2 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 170 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2DIR _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 8 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 92 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9NXG2 _struct_ref_seq.db_align_beg 170 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 254 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 8 _struct_ref_seq.pdbx_auth_seq_align_end 92 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 2DIR GLY A 1 ? UNP Q9NXG2 ? ? 'cloning artifact' 1 1 1 2DIR SER A 2 ? UNP Q9NXG2 ? ? 'cloning artifact' 2 2 1 2DIR SER A 3 ? UNP Q9NXG2 ? ? 'cloning artifact' 3 3 1 2DIR GLY A 4 ? UNP Q9NXG2 ? ? 'cloning artifact' 4 4 1 2DIR SER A 5 ? UNP Q9NXG2 ? ? 'cloning artifact' 5 5 1 2DIR SER A 6 ? UNP Q9NXG2 ? ? 'cloning artifact' 6 6 1 2DIR GLY A 7 ? UNP Q9NXG2 ? ? 'cloning artifact' 7 7 1 2DIR SER A 93 ? UNP Q9NXG2 ? ? 'cloning artifact' 93 8 1 2DIR GLY A 94 ? UNP Q9NXG2 ? ? 'cloning artifact' 94 9 1 2DIR PRO A 95 ? UNP Q9NXG2 ? ? 'cloning artifact' 95 10 1 2DIR SER A 96 ? UNP Q9NXG2 ? ? 'cloning artifact' 96 11 1 2DIR SER A 97 ? UNP Q9NXG2 ? ? 'cloning artifact' 97 12 1 2DIR GLY A 98 ? UNP Q9NXG2 ? ? 'cloning artifact' 98 13 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? '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 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 3D_15N-separated_NOESY 1 2 1 3D_13C-separated_NOESY 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength 120mM _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.type ? # _pdbx_nmr_refine.entry_id 2DIR _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 2DIR _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'target function, structures with the lowest energy, structures with the least restraint violations' _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 2DIR _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal collection XwinNMR 2.6 Bruker 1 processing NMRPipe 20031121 Delaglio,F. 2 'data analysis' NMRView 5.0.4 Johnson,B.A. 3 'data analysis' KUJIRA 0.9321 Kobayashi,N. 4 'structure solution' CYANA 2.0.17 Guntert,P. 5 refinement CYANA 2.0.17 Guntert,P. 6 # _exptl.entry_id 2DIR _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2DIR _struct.title 'Solution structure of the THUMP domain of THUMP domain-containing protein 1' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2DIR _struct_keywords.pdbx_keywords 'RNA BINDING PROTEIN' _struct_keywords.text ;THUMP domain, THUMP domain-containing protein 1, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, RNA 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 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ALA A 9 ? PHE A 26 ? ALA A 9 PHE A 26 1 ? 18 HELX_P HELX_P2 2 ARG A 48 ? LEU A 62 ? ARG A 48 LEU A 62 1 ? 15 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 1 -0.01 2 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 2 0.04 3 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 3 0.01 4 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 4 -0.01 5 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 5 0.01 6 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 6 -0.01 7 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 7 0.01 8 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 8 0.05 9 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 9 -0.06 10 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 10 0.06 11 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 11 0.07 12 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 12 0.01 13 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 13 0.08 14 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 14 0.04 15 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 15 0.07 16 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 16 -0.04 17 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 17 -0.06 18 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 18 -0.01 19 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 19 0.01 20 ALA 28 A . ? ALA 28 A PRO 29 A ? PRO 29 A 20 0.05 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 4 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? parallel A 2 3 ? parallel A 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 LYS A 67 ? VAL A 68 ? LYS A 67 VAL A 68 A 2 THR A 33 ? LYS A 39 ? THR A 33 LYS A 39 A 3 TYR A 75 ? ILE A 81 ? TYR A 75 ILE A 81 A 4 CYS A 86 ? LYS A 92 ? CYS A 86 LYS A 92 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O LYS A 67 ? O LYS A 67 N PHE A 34 ? N PHE A 34 A 2 3 N VAL A 37 ? N VAL A 37 O VAL A 79 ? O VAL A 79 A 3 4 N GLU A 80 ? N GLU A 80 O CYS A 87 ? O CYS A 87 # _database_PDB_matrix.entry_id 2DIR _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 2DIR _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 GLY 1 1 1 GLY GLY A . n A 1 2 SER 2 2 2 SER SER A . n A 1 3 SER 3 3 3 SER SER A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 SER 5 5 5 SER SER A . n A 1 6 SER 6 6 6 SER SER A . n A 1 7 GLY 7 7 7 GLY GLY A . n A 1 8 LYS 8 8 8 LYS LYS A . n A 1 9 ALA 9 9 9 ALA ALA A . n A 1 10 PHE 10 10 10 PHE PHE A . n A 1 11 LEU 11 11 11 LEU LEU A . n A 1 12 GLU 12 12 12 GLU GLU A . n A 1 13 ASP 13 13 13 ASP ASP A . n A 1 14 MET 14 14 14 MET MET A . n A 1 15 LYS 15 15 15 LYS LYS A . n A 1 16 LYS 16 16 16 LYS LYS A . n A 1 17 TYR 17 17 17 TYR TYR A . n A 1 18 ALA 18 18 18 ALA ALA A . n A 1 19 GLU 19 19 19 GLU GLU A . n A 1 20 THR 20 20 20 THR THR A . n A 1 21 PHE 21 21 21 PHE PHE A . n A 1 22 LEU 22 22 22 LEU LEU A . n A 1 23 GLU 23 23 23 GLU GLU A . n A 1 24 PRO 24 24 24 PRO PRO A . n A 1 25 TRP 25 25 25 TRP TRP A . n A 1 26 PHE 26 26 26 PHE PHE A . n A 1 27 LYS 27 27 27 LYS LYS A . n A 1 28 ALA 28 28 28 ALA ALA A . n A 1 29 PRO 29 29 29 PRO PRO A . n A 1 30 ASN 30 30 30 ASN ASN A . n A 1 31 LYS 31 31 31 LYS LYS A . n A 1 32 GLY 32 32 32 GLY GLY A . n A 1 33 THR 33 33 33 THR THR A . n A 1 34 PHE 34 34 34 PHE PHE A . n A 1 35 GLN 35 35 35 GLN GLN A . n A 1 36 ILE 36 36 36 ILE ILE A . n A 1 37 VAL 37 37 37 VAL VAL A . n A 1 38 TYR 38 38 38 TYR TYR A . n A 1 39 LYS 39 39 39 LYS LYS A . n A 1 40 SER 40 40 40 SER SER A . n A 1 41 ARG 41 41 41 ARG ARG A . n A 1 42 ASN 42 42 42 ASN ASN A . n A 1 43 ASN 43 43 43 ASN ASN A . n A 1 44 SER 44 44 44 SER SER A . n A 1 45 HIS 45 45 45 HIS HIS A . n A 1 46 VAL 46 46 46 VAL VAL A . n A 1 47 ASN 47 47 47 ASN ASN A . n A 1 48 ARG 48 48 48 ARG ARG A . n A 1 49 GLU 49 49 49 GLU GLU A . n A 1 50 GLU 50 50 50 GLU GLU A . n A 1 51 VAL 51 51 51 VAL VAL A . n A 1 52 ILE 52 52 52 ILE ILE A . n A 1 53 ARG 53 53 53 ARG ARG A . n A 1 54 GLU 54 54 54 GLU GLU A . n A 1 55 LEU 55 55 55 LEU LEU A . n A 1 56 ALA 56 56 56 ALA ALA A . n A 1 57 GLY 57 57 57 GLY GLY A . n A 1 58 ILE 58 58 58 ILE ILE A . n A 1 59 VAL 59 59 59 VAL VAL A . n A 1 60 CYS 60 60 60 CYS CYS A . n A 1 61 THR 61 61 61 THR THR A . n A 1 62 LEU 62 62 62 LEU LEU A . n A 1 63 ASN 63 63 63 ASN ASN A . n A 1 64 SER 64 64 64 SER SER A . n A 1 65 GLU 65 65 65 GLU GLU A . n A 1 66 ASN 66 66 66 ASN ASN A . n A 1 67 LYS 67 67 67 LYS LYS A . n A 1 68 VAL 68 68 68 VAL VAL A . n A 1 69 ASP 69 69 69 ASP ASP A . n A 1 70 LEU 70 70 70 LEU LEU A . n A 1 71 THR 71 71 71 THR THR A . n A 1 72 ASN 72 72 72 ASN ASN A . n A 1 73 PRO 73 73 73 PRO PRO A . n A 1 74 GLN 74 74 74 GLN GLN A . n A 1 75 TYR 75 75 75 TYR TYR A . n A 1 76 THR 76 76 76 THR THR A . n A 1 77 VAL 77 77 77 VAL VAL A . n A 1 78 VAL 78 78 78 VAL VAL A . n A 1 79 VAL 79 79 79 VAL VAL A . n A 1 80 GLU 80 80 80 GLU GLU A . n A 1 81 ILE 81 81 81 ILE ILE A . n A 1 82 ILE 82 82 82 ILE ILE A . n A 1 83 LYS 83 83 83 LYS LYS A . n A 1 84 ALA 84 84 84 ALA ALA A . n A 1 85 VAL 85 85 85 VAL VAL A . n A 1 86 CYS 86 86 86 CYS CYS A . n A 1 87 CYS 87 87 87 CYS CYS A . n A 1 88 LEU 88 88 88 LEU LEU A . n A 1 89 SER 89 89 89 SER SER A . n A 1 90 VAL 90 90 90 VAL VAL A . n A 1 91 VAL 91 91 91 VAL VAL A . n A 1 92 LYS 92 92 92 LYS LYS A . n A 1 93 SER 93 93 93 SER SER A . n A 1 94 GLY 94 94 94 GLY GLY A . n A 1 95 PRO 95 95 95 PRO PRO A . n A 1 96 SER 96 96 96 SER SER A . n A 1 97 SER 97 97 97 SER SER A . n A 1 98 GLY 98 98 98 GLY GLY A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'NPPSFA, National Project on Protein Structural and Functional Analyses' _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # _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 2006-09-30 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 # _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_nmr_spectrometer 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 4 'Structure model' struct_ref_seq_dif # 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' 4 4 'Structure model' '_pdbx_nmr_spectrometer.model' 5 4 'Structure model' '_struct_ref_seq_dif.details' # 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 SER A 6 ? ? -56.95 -179.84 2 1 PHE A 10 ? ? -38.54 -37.03 3 1 GLU A 19 ? ? -75.37 -70.72 4 1 PHE A 26 ? ? -131.57 -44.24 5 1 ALA A 28 ? ? -41.80 158.01 6 1 ASN A 72 ? ? -119.56 55.17 7 2 SER A 2 ? ? -85.36 47.68 8 2 LYS A 15 ? ? -35.50 -71.96 9 2 GLU A 19 ? ? -69.15 -71.06 10 2 PHE A 26 ? ? -131.24 -42.80 11 2 ALA A 28 ? ? -41.91 157.62 12 2 ASN A 43 ? ? -172.44 123.68 13 2 LEU A 55 ? ? -38.78 -33.90 14 2 LYS A 83 ? ? 70.80 42.03 15 3 GLU A 19 ? ? -65.67 -71.08 16 3 PHE A 26 ? ? -130.68 -42.73 17 3 ALA A 28 ? ? -41.91 157.50 18 3 ASN A 42 ? ? -57.00 170.91 19 3 VAL A 46 ? ? -49.43 156.95 20 3 ASN A 47 ? ? -34.55 101.92 21 3 LEU A 55 ? ? -36.85 -30.73 22 3 ASN A 72 ? ? -119.37 55.25 23 4 ALA A 18 ? ? -38.06 -34.07 24 4 GLU A 19 ? ? -71.73 -71.21 25 4 ALA A 28 ? ? -42.71 157.43 26 4 VAL A 59 ? ? -38.84 -33.05 27 4 SER A 93 ? ? -125.96 -58.61 28 5 GLU A 19 ? ? -53.80 -70.35 29 5 PHE A 26 ? ? -130.71 -43.75 30 5 ALA A 28 ? ? -41.92 158.38 31 5 ASN A 42 ? ? 39.64 42.18 32 5 ASN A 43 ? ? 34.73 45.34 33 5 SER A 44 ? ? -34.61 135.65 34 5 VAL A 46 ? ? -34.16 139.41 35 5 VAL A 59 ? ? -33.58 -39.16 36 5 LYS A 83 ? ? 70.64 47.51 37 6 GLU A 12 ? ? -37.54 -28.36 38 6 LYS A 16 ? ? -63.11 -71.17 39 6 PHE A 26 ? ? -131.83 -42.35 40 6 ALA A 28 ? ? -41.66 157.17 41 6 ASN A 42 ? ? -46.35 166.89 42 6 HIS A 45 ? ? -100.40 -64.92 43 6 ASN A 47 ? ? -49.77 174.57 44 6 LEU A 55 ? ? -34.97 -33.96 45 6 ALA A 84 ? ? 73.78 43.45 46 6 PRO A 95 ? ? -69.75 86.37 47 6 SER A 96 ? ? -172.91 132.62 48 6 SER A 97 ? ? -121.94 -62.12 49 7 GLU A 19 ? ? -65.74 -71.00 50 7 ALA A 28 ? ? -41.37 156.85 51 7 LEU A 55 ? ? -34.76 -39.68 52 8 PHE A 10 ? ? -38.06 -37.93 53 8 LYS A 16 ? ? -63.35 -71.17 54 8 GLU A 19 ? ? -54.35 -70.71 55 8 ALA A 28 ? ? -41.82 156.76 56 8 ARG A 41 ? ? -125.14 -62.45 57 9 SER A 6 ? ? -49.37 163.05 58 9 ALA A 9 ? ? -37.34 -28.72 59 9 ASP A 13 ? ? -64.61 -70.32 60 9 ALA A 18 ? ? -37.45 -28.39 61 9 GLU A 19 ? ? -74.89 -70.55 62 9 ALA A 28 ? ? -41.44 156.94 63 9 ARG A 41 ? ? -124.38 -64.02 64 9 SER A 44 ? ? -122.05 -71.80 65 9 ILE A 52 ? ? -64.54 -72.92 66 9 LEU A 55 ? ? -36.98 -39.88 67 10 SER A 6 ? ? -84.59 42.94 68 10 ALA A 18 ? ? -34.33 -35.34 69 10 GLU A 19 ? ? -71.05 -70.93 70 10 ALA A 28 ? ? -42.03 158.04 71 10 ASN A 43 ? ? -170.49 140.78 72 10 ASN A 47 ? ? -54.98 104.15 73 10 LEU A 55 ? ? -34.21 -39.85 74 10 PRO A 95 ? ? -69.79 2.88 75 11 GLU A 12 ? ? -37.61 -34.12 76 11 ALA A 18 ? ? -35.79 -33.39 77 11 GLU A 19 ? ? -71.99 -70.98 78 11 PHE A 26 ? ? -131.59 -42.69 79 11 ALA A 28 ? ? -41.58 156.95 80 11 ASN A 43 ? ? -104.48 -61.78 81 11 VAL A 46 ? ? -36.87 150.76 82 11 ASN A 47 ? ? -42.33 163.70 83 11 ARG A 48 ? ? -106.67 -63.49 84 12 LYS A 8 ? ? -164.67 112.10 85 12 ALA A 9 ? ? -37.44 -34.78 86 12 GLU A 19 ? ? -62.82 -71.34 87 12 PHE A 26 ? ? -132.90 -42.59 88 12 ALA A 28 ? ? -41.82 157.61 89 12 ARG A 41 ? ? -57.52 173.15 90 12 HIS A 45 ? ? -107.60 -60.17 91 12 ILE A 52 ? ? -67.80 -72.56 92 12 VAL A 59 ? ? -37.45 -34.70 93 12 ASN A 72 ? ? -118.02 51.73 94 13 ALA A 28 ? ? -41.81 157.49 95 13 ASN A 42 ? ? -58.10 171.01 96 13 HIS A 45 ? ? -123.63 -60.24 97 13 ASN A 47 ? ? -55.07 92.71 98 13 ILE A 52 ? ? -58.99 -73.66 99 13 ASN A 72 ? ? -117.41 51.70 100 13 ALA A 84 ? ? 70.06 44.01 101 14 MET A 14 ? ? -38.44 -30.99 102 14 GLU A 19 ? ? -75.10 -70.81 103 14 PHE A 26 ? ? -130.48 -42.68 104 14 ALA A 28 ? ? -41.83 157.52 105 14 ASN A 47 ? ? -58.15 -176.09 106 14 LEU A 55 ? ? -34.97 -38.47 107 14 THR A 71 ? ? -109.01 -60.20 108 14 ASN A 72 ? ? -117.64 56.54 109 15 LYS A 8 ? ? -164.26 113.90 110 15 GLU A 19 ? ? -64.70 -71.34 111 15 THR A 20 ? ? -48.16 -19.67 112 15 ALA A 28 ? ? -41.78 157.79 113 15 ASN A 43 ? ? -34.23 129.89 114 15 SER A 44 ? ? -107.94 74.73 115 15 ASN A 47 ? ? -59.55 176.68 116 15 LEU A 55 ? ? -34.13 -39.16 117 15 ASN A 72 ? ? -119.31 55.88 118 16 ALA A 18 ? ? -38.84 -33.87 119 16 PHE A 26 ? ? -132.13 -42.96 120 16 ALA A 28 ? ? -41.74 158.27 121 16 ILE A 52 ? ? -60.38 -71.54 122 16 ALA A 84 ? ? 71.05 41.36 123 17 SER A 5 ? ? -49.58 165.20 124 17 LYS A 15 ? ? -35.72 -71.07 125 17 GLU A 19 ? ? -69.39 -70.99 126 17 PHE A 26 ? ? -133.94 -42.52 127 17 ALA A 28 ? ? -41.83 157.79 128 17 SER A 44 ? ? -78.95 -73.98 129 17 VAL A 46 ? ? -173.92 135.63 130 17 ASN A 47 ? ? -36.70 99.55 131 17 ALA A 84 ? ? 70.64 39.90 132 17 PRO A 95 ? ? -69.75 91.02 133 18 SER A 6 ? ? -108.45 42.11 134 18 GLU A 19 ? ? -74.94 -70.51 135 18 ALA A 28 ? ? -41.79 158.31 136 18 ALA A 84 ? ? 72.21 43.38 137 19 ALA A 9 ? ? -37.38 -30.55 138 19 GLU A 19 ? ? -62.83 -71.16 139 19 THR A 20 ? ? -49.89 -17.74 140 19 ALA A 28 ? ? -41.81 158.17 141 19 ASN A 47 ? ? -57.56 104.27 142 20 SER A 5 ? ? -132.95 -54.43 143 20 ALA A 18 ? ? -39.33 -37.12 144 20 GLU A 19 ? ? -72.41 -71.14 145 20 ALA A 28 ? ? -41.87 157.51 146 20 ARG A 41 ? ? -127.56 -58.69 147 20 ASN A 43 ? ? -38.35 103.78 148 20 ILE A 52 ? ? -52.56 -71.21 149 20 VAL A 59 ? ? -39.53 -36.48 150 20 THR A 61 ? ? -39.09 -27.64 151 20 ASN A 72 ? ? -119.42 54.70 152 20 LYS A 83 ? ? 74.70 46.48 #