data_2D93 # _entry.id 2D93 # _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 2D93 pdb_00002d93 10.2210/pdb2d93/pdb RCSB RCSB025140 ? ? WWPDB D_1000025140 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id hsk003000463.1 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2D93 _pdbx_database_status.recvd_initial_deposition_date 2005-12-08 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _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 'Inoue, K.' 1 'Muto, Y.' 2 'Hayashi, F.' 3 'Yokoyama, S.' 4 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 5 # _citation.id primary _citation.title 'Solution structure of the cNMP_binding domain of human Rap guanine nucleotide exchange factor 6' _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 'Inoue, K.' 1 ? primary 'Muto, Y.' 2 ? primary 'Hayashi, F.' 3 ? primary 'Yokoyama, S.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'Rap guanine nucleotide exchange factor 6' _entity.formula_weight 14927.764 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'cNMP_binding domain' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'PDZ domain containing guanine nucleotide exchange factor 2, PDZ-GEF2, RA-GEF-2' # _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 ;GSSGSSGDDDIEQLLEFMHQLPAFANMTMSVRRELCSVMIFEVVEQAGAIILEDGQELDSWYVILNGTVEISHPDGKVEN LFMGNSFGITPTLDKQYMHGIVRTKVDDCQFVCIAQQDYWRILNHVEKSGPSSG ; _entity_poly.pdbx_seq_one_letter_code_can ;GSSGSSGDDDIEQLLEFMHQLPAFANMTMSVRRELCSVMIFEVVEQAGAIILEDGQELDSWYVILNGTVEISHPDGKVEN LFMGNSFGITPTLDKQYMHGIVRTKVDDCQFVCIAQQDYWRILNHVEKSGPSSG ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier hsk003000463.1 # 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 ASP n 1 9 ASP n 1 10 ASP n 1 11 ILE n 1 12 GLU n 1 13 GLN n 1 14 LEU n 1 15 LEU n 1 16 GLU n 1 17 PHE n 1 18 MET n 1 19 HIS n 1 20 GLN n 1 21 LEU n 1 22 PRO n 1 23 ALA n 1 24 PHE n 1 25 ALA n 1 26 ASN n 1 27 MET n 1 28 THR n 1 29 MET n 1 30 SER n 1 31 VAL n 1 32 ARG n 1 33 ARG n 1 34 GLU n 1 35 LEU n 1 36 CYS n 1 37 SER n 1 38 VAL n 1 39 MET n 1 40 ILE n 1 41 PHE n 1 42 GLU n 1 43 VAL n 1 44 VAL n 1 45 GLU n 1 46 GLN n 1 47 ALA n 1 48 GLY n 1 49 ALA n 1 50 ILE n 1 51 ILE n 1 52 LEU n 1 53 GLU n 1 54 ASP n 1 55 GLY n 1 56 GLN n 1 57 GLU n 1 58 LEU n 1 59 ASP n 1 60 SER n 1 61 TRP n 1 62 TYR n 1 63 VAL n 1 64 ILE n 1 65 LEU n 1 66 ASN n 1 67 GLY n 1 68 THR n 1 69 VAL n 1 70 GLU n 1 71 ILE n 1 72 SER n 1 73 HIS n 1 74 PRO n 1 75 ASP n 1 76 GLY n 1 77 LYS n 1 78 VAL n 1 79 GLU n 1 80 ASN n 1 81 LEU n 1 82 PHE n 1 83 MET n 1 84 GLY n 1 85 ASN n 1 86 SER n 1 87 PHE n 1 88 GLY n 1 89 ILE n 1 90 THR n 1 91 PRO n 1 92 THR n 1 93 LEU n 1 94 ASP n 1 95 LYS n 1 96 GLN n 1 97 TYR n 1 98 MET n 1 99 HIS n 1 100 GLY n 1 101 ILE n 1 102 VAL n 1 103 ARG n 1 104 THR n 1 105 LYS n 1 106 VAL n 1 107 ASP n 1 108 ASP n 1 109 CYS n 1 110 GLN n 1 111 PHE n 1 112 VAL n 1 113 CYS n 1 114 ILE n 1 115 ALA n 1 116 GLN n 1 117 GLN n 1 118 ASP n 1 119 TYR n 1 120 TRP n 1 121 ARG n 1 122 ILE n 1 123 LEU n 1 124 ASN n 1 125 HIS n 1 126 VAL n 1 127 GLU n 1 128 LYS n 1 129 SER n 1 130 GLY n 1 131 PRO n 1 132 SER n 1 133 SER n 1 134 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 'KAZUSA cDNA ha02566' _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 ? _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 P050404-16 _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 RPGF6_HUMAN _struct_ref.pdbx_db_accession Q8TEU7 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;DDDIEQLLEFMHQLPAFANMTMSVRRELCSVMIFEVVEQAGAIILEDGQELDSWYVILNGTVEISHPDGKVENLFMGNSF GITPTLDKQYMHGIVRTKVDDCQFVCIAQQDYWRILNHVEK ; _struct_ref.pdbx_align_begin 265 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2D93 _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 128 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q8TEU7 _struct_ref_seq.db_align_beg 265 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 385 _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 128 # 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 2D93 GLY A 1 ? UNP Q8TEU7 ? ? 'cloning artifact' 1 1 1 2D93 SER A 2 ? UNP Q8TEU7 ? ? 'cloning artifact' 2 2 1 2D93 SER A 3 ? UNP Q8TEU7 ? ? 'cloning artifact' 3 3 1 2D93 GLY A 4 ? UNP Q8TEU7 ? ? 'cloning artifact' 4 4 1 2D93 SER A 5 ? UNP Q8TEU7 ? ? 'cloning artifact' 5 5 1 2D93 SER A 6 ? UNP Q8TEU7 ? ? 'cloning artifact' 6 6 1 2D93 GLY A 7 ? UNP Q8TEU7 ? ? 'cloning artifact' 7 7 1 2D93 SER A 129 ? UNP Q8TEU7 ? ? 'cloning artifact' 129 8 1 2D93 GLY A 130 ? UNP Q8TEU7 ? ? 'cloning artifact' 130 9 1 2D93 PRO A 131 ? UNP Q8TEU7 ? ? 'cloning artifact' 131 10 1 2D93 SER A 132 ? UNP Q8TEU7 ? ? 'cloning artifact' 132 11 1 2D93 SER A 133 ? UNP Q8TEU7 ? ? 'cloning artifact' 133 12 1 2D93 GLY A 134 ? UNP Q8TEU7 ? ? 'cloning artifact' 134 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 '1.06mM U-15N, 13C-labeled protein; 20mM d-Tris-HCl; 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 2D93 _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 2D93 _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 2D93 _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 3.5 ? 1 processing NMRPipe 20031121 'Delaglio, F.' 2 'data analysis' NMRView 5.0.4 'Johnson, B.A.' 3 'data analysis' KUJIRA 0.93191 'Kobayashi, N.' 4 'structure solution' CYANA 2.0.17 'Guntert, P.' 5 refinement CYANA 2.0.17 'Guntert, P.' 6 # _exptl.entry_id 2D93 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2D93 _struct.title 'Solution structure of the cNMP_binding domain of human Rap guanine nucleotide exchange factor 6' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2D93 _struct_keywords.pdbx_keywords 'SIGNALING PROTEIN' _struct_keywords.text ;cNMP_binding domain, Rap guanine nucleotide exchange factor 6, PDZ domain containing guanine nucleotide exchange factor 2, PDZ-GEF2, RA-GEF-2, RAPGEF6, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SIGNALING 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 ASP A 9 ? LEU A 21 ? ASP A 9 LEU A 21 1 ? 13 HELX_P HELX_P2 2 THR A 28 ? CYS A 36 ? THR A 28 CYS A 36 1 ? 9 HELX_P HELX_P3 3 GLN A 116 ? LEU A 123 ? GLN A 116 LEU A 123 1 ? 8 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 4 ? C ? 2 ? # 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 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel C 1 2 ? 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 MET A 39 ? VAL A 44 ? MET A 39 VAL A 44 A 2 CYS A 109 ? ALA A 115 ? CYS A 109 ALA A 115 A 3 SER A 60 ? VAL A 63 ? SER A 60 VAL A 63 A 4 SER A 86 ? PHE A 87 ? SER A 86 PHE A 87 B 1 ILE A 50 ? LEU A 52 ? ILE A 50 LEU A 52 B 2 ILE A 101 ? THR A 104 ? ILE A 101 THR A 104 B 3 VAL A 69 ? SER A 72 ? VAL A 69 SER A 72 B 4 VAL A 78 ? LEU A 81 ? VAL A 78 LEU A 81 C 1 GLU A 57 ? LEU A 58 ? GLU A 57 LEU A 58 C 2 GLN A 96 ? TYR A 97 ? GLN A 96 TYR A 97 # 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 N ILE A 40 ? N ILE A 40 O CYS A 113 ? O CYS A 113 A 2 3 O ILE A 114 ? O ILE A 114 N TRP A 61 ? N TRP A 61 A 3 4 N TYR A 62 ? N TYR A 62 O PHE A 87 ? O PHE A 87 B 1 2 N LEU A 52 ? N LEU A 52 O VAL A 102 ? O VAL A 102 B 2 3 O ARG A 103 ? O ARG A 103 N GLU A 70 ? N GLU A 70 B 3 4 N ILE A 71 ? N ILE A 71 O GLU A 79 ? O GLU A 79 C 1 2 N LEU A 58 ? N LEU A 58 O GLN A 96 ? O GLN A 96 # _database_PDB_matrix.entry_id 2D93 _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 2D93 _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 ASP 8 8 8 ASP ASP A . n A 1 9 ASP 9 9 9 ASP ASP A . n A 1 10 ASP 10 10 10 ASP ASP A . n A 1 11 ILE 11 11 11 ILE ILE A . n A 1 12 GLU 12 12 12 GLU GLU A . n A 1 13 GLN 13 13 13 GLN GLN A . n A 1 14 LEU 14 14 14 LEU LEU A . n A 1 15 LEU 15 15 15 LEU LEU A . n A 1 16 GLU 16 16 16 GLU GLU A . n A 1 17 PHE 17 17 17 PHE PHE A . n A 1 18 MET 18 18 18 MET MET A . n A 1 19 HIS 19 19 19 HIS HIS A . n A 1 20 GLN 20 20 20 GLN GLN A . n A 1 21 LEU 21 21 21 LEU LEU A . n A 1 22 PRO 22 22 22 PRO PRO A . n A 1 23 ALA 23 23 23 ALA ALA A . n A 1 24 PHE 24 24 24 PHE PHE A . n A 1 25 ALA 25 25 25 ALA ALA A . n A 1 26 ASN 26 26 26 ASN ASN A . n A 1 27 MET 27 27 27 MET MET A . n A 1 28 THR 28 28 28 THR THR A . n A 1 29 MET 29 29 29 MET MET A . n A 1 30 SER 30 30 30 SER SER A . n A 1 31 VAL 31 31 31 VAL VAL A . n A 1 32 ARG 32 32 32 ARG ARG A . n A 1 33 ARG 33 33 33 ARG ARG A . n A 1 34 GLU 34 34 34 GLU GLU A . n A 1 35 LEU 35 35 35 LEU LEU A . n A 1 36 CYS 36 36 36 CYS CYS A . n A 1 37 SER 37 37 37 SER SER A . n A 1 38 VAL 38 38 38 VAL VAL A . n A 1 39 MET 39 39 39 MET MET A . n A 1 40 ILE 40 40 40 ILE ILE A . n A 1 41 PHE 41 41 41 PHE PHE A . n A 1 42 GLU 42 42 42 GLU GLU A . n A 1 43 VAL 43 43 43 VAL VAL A . n A 1 44 VAL 44 44 44 VAL VAL A . n A 1 45 GLU 45 45 45 GLU GLU A . n A 1 46 GLN 46 46 46 GLN GLN A . n A 1 47 ALA 47 47 47 ALA ALA A . n A 1 48 GLY 48 48 48 GLY GLY A . n A 1 49 ALA 49 49 49 ALA ALA A . n A 1 50 ILE 50 50 50 ILE ILE A . n A 1 51 ILE 51 51 51 ILE ILE A . n A 1 52 LEU 52 52 52 LEU LEU A . n A 1 53 GLU 53 53 53 GLU GLU A . n A 1 54 ASP 54 54 54 ASP ASP A . n A 1 55 GLY 55 55 55 GLY GLY A . n A 1 56 GLN 56 56 56 GLN GLN A . n A 1 57 GLU 57 57 57 GLU GLU A . n A 1 58 LEU 58 58 58 LEU LEU A . n A 1 59 ASP 59 59 59 ASP ASP A . n A 1 60 SER 60 60 60 SER SER A . n A 1 61 TRP 61 61 61 TRP TRP A . n A 1 62 TYR 62 62 62 TYR TYR A . n A 1 63 VAL 63 63 63 VAL VAL A . n A 1 64 ILE 64 64 64 ILE ILE A . n A 1 65 LEU 65 65 65 LEU LEU A . n A 1 66 ASN 66 66 66 ASN ASN A . n A 1 67 GLY 67 67 67 GLY GLY A . n A 1 68 THR 68 68 68 THR THR A . n A 1 69 VAL 69 69 69 VAL VAL A . n A 1 70 GLU 70 70 70 GLU GLU A . n A 1 71 ILE 71 71 71 ILE ILE A . n A 1 72 SER 72 72 72 SER SER A . n A 1 73 HIS 73 73 73 HIS HIS A . n A 1 74 PRO 74 74 74 PRO PRO A . n A 1 75 ASP 75 75 75 ASP ASP A . n A 1 76 GLY 76 76 76 GLY GLY A . n A 1 77 LYS 77 77 77 LYS LYS A . n A 1 78 VAL 78 78 78 VAL VAL A . n A 1 79 GLU 79 79 79 GLU GLU A . n A 1 80 ASN 80 80 80 ASN ASN A . n A 1 81 LEU 81 81 81 LEU LEU A . n A 1 82 PHE 82 82 82 PHE PHE A . n A 1 83 MET 83 83 83 MET MET A . n A 1 84 GLY 84 84 84 GLY GLY A . n A 1 85 ASN 85 85 85 ASN ASN A . n A 1 86 SER 86 86 86 SER SER A . n A 1 87 PHE 87 87 87 PHE PHE A . n A 1 88 GLY 88 88 88 GLY GLY A . n A 1 89 ILE 89 89 89 ILE ILE A . n A 1 90 THR 90 90 90 THR THR A . n A 1 91 PRO 91 91 91 PRO PRO A . n A 1 92 THR 92 92 92 THR THR A . n A 1 93 LEU 93 93 93 LEU LEU A . n A 1 94 ASP 94 94 94 ASP ASP A . n A 1 95 LYS 95 95 95 LYS LYS A . n A 1 96 GLN 96 96 96 GLN GLN A . n A 1 97 TYR 97 97 97 TYR TYR A . n A 1 98 MET 98 98 98 MET MET A . n A 1 99 HIS 99 99 99 HIS HIS A . n A 1 100 GLY 100 100 100 GLY GLY A . n A 1 101 ILE 101 101 101 ILE ILE A . n A 1 102 VAL 102 102 102 VAL VAL A . n A 1 103 ARG 103 103 103 ARG ARG A . n A 1 104 THR 104 104 104 THR THR A . n A 1 105 LYS 105 105 105 LYS LYS A . n A 1 106 VAL 106 106 106 VAL VAL A . n A 1 107 ASP 107 107 107 ASP ASP A . n A 1 108 ASP 108 108 108 ASP ASP A . n A 1 109 CYS 109 109 109 CYS CYS A . n A 1 110 GLN 110 110 110 GLN GLN A . n A 1 111 PHE 111 111 111 PHE PHE A . n A 1 112 VAL 112 112 112 VAL VAL A . n A 1 113 CYS 113 113 113 CYS CYS A . n A 1 114 ILE 114 114 114 ILE ILE A . n A 1 115 ALA 115 115 115 ALA ALA A . n A 1 116 GLN 116 116 116 GLN GLN A . n A 1 117 GLN 117 117 117 GLN GLN A . n A 1 118 ASP 118 118 118 ASP ASP A . n A 1 119 TYR 119 119 119 TYR TYR A . n A 1 120 TRP 120 120 120 TRP TRP A . n A 1 121 ARG 121 121 121 ARG ARG A . n A 1 122 ILE 122 122 122 ILE ILE A . n A 1 123 LEU 123 123 123 LEU LEU A . n A 1 124 ASN 124 124 124 ASN ASN A . n A 1 125 HIS 125 125 125 HIS HIS A . n A 1 126 VAL 126 126 126 VAL VAL A . n A 1 127 GLU 127 127 127 GLU GLU A . n A 1 128 LYS 128 128 128 LYS LYS A . n A 1 129 SER 129 129 129 SER SER A . n A 1 130 GLY 130 130 130 GLY GLY A . n A 1 131 PRO 131 131 131 PRO PRO A . n A 1 132 SER 132 132 132 SER SER A . n A 1 133 SER 133 133 133 SER SER A . n A 1 134 GLY 134 134 134 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 2006-06-08 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 ALA A 47 ? ? -50.05 -178.59 2 1 GLU A 57 ? ? -63.34 95.59 3 1 MET A 83 ? ? -35.32 120.49 4 1 PRO A 91 ? ? -69.83 2.92 5 1 ILE A 122 ? ? -103.37 -63.82 6 1 HIS A 125 ? ? -111.49 65.99 7 2 GLU A 57 ? ? -56.73 104.98 8 2 MET A 83 ? ? -39.30 119.69 9 2 PRO A 91 ? ? -69.72 2.81 10 2 ASP A 94 ? ? -52.70 171.08 11 2 ILE A 122 ? ? -96.56 -71.63 12 2 PRO A 131 ? ? -69.76 88.80 13 3 ASP A 8 ? ? -131.25 -54.96 14 3 ASP A 9 ? ? -99.06 43.18 15 3 GLU A 57 ? ? -54.05 92.63 16 3 MET A 83 ? ? -37.68 118.62 17 3 ASN A 85 ? ? -61.41 -179.39 18 3 PRO A 91 ? ? -69.74 2.65 19 3 ILE A 122 ? ? -122.68 -54.49 20 3 GLU A 127 ? ? -34.90 140.82 21 3 SER A 129 ? ? -38.99 99.21 22 4 ARG A 32 ? ? -48.16 -72.30 23 4 GLU A 57 ? ? -53.59 101.12 24 4 PRO A 91 ? ? -69.75 2.97 25 4 MET A 98 ? ? -49.31 104.30 26 4 HIS A 99 ? ? -82.35 40.91 27 4 HIS A 125 ? ? -110.59 56.02 28 5 ASP A 8 ? ? -127.88 -50.74 29 5 ASP A 9 ? ? -114.02 74.17 30 5 ARG A 32 ? ? -48.60 -72.91 31 5 ASP A 54 ? ? -59.00 106.59 32 5 GLU A 57 ? ? -44.46 95.56 33 5 PRO A 91 ? ? -69.77 2.77 34 5 LEU A 93 ? ? -36.97 -31.86 35 5 HIS A 99 ? ? -95.83 46.37 36 6 GLU A 57 ? ? -53.74 100.72 37 6 PRO A 91 ? ? -69.76 2.40 38 6 HIS A 99 ? ? -95.82 40.95 39 6 ASN A 124 ? ? -54.34 -175.89 40 6 GLU A 127 ? ? -69.86 71.57 41 6 SER A 129 ? ? -173.24 -179.31 42 6 PRO A 131 ? ? -69.78 87.09 43 7 SER A 3 ? ? -67.98 92.75 44 7 GLU A 16 ? ? -36.09 -37.96 45 7 GLU A 57 ? ? -38.49 109.39 46 7 MET A 83 ? ? -35.03 120.08 47 7 ASN A 85 ? ? -52.49 179.38 48 7 PRO A 91 ? ? -69.75 2.99 49 7 LEU A 93 ? ? -36.42 -30.80 50 7 HIS A 125 ? ? -109.28 40.73 51 7 LYS A 128 ? ? -50.24 178.75 52 8 THR A 28 ? ? -51.91 175.73 53 8 GLU A 57 ? ? -61.02 94.00 54 8 MET A 83 ? ? -38.65 120.56 55 8 PRO A 91 ? ? -69.78 3.38 56 8 LEU A 93 ? ? -36.82 -29.97 57 8 HIS A 125 ? ? -107.55 56.82 58 8 LYS A 128 ? ? -171.62 149.95 59 9 SER A 5 ? ? -83.59 41.94 60 9 GLU A 16 ? ? -39.69 -28.97 61 9 ALA A 47 ? ? -54.84 178.61 62 9 GLU A 57 ? ? -58.48 88.36 63 9 ILE A 64 ? ? -54.00 104.89 64 9 PRO A 91 ? ? -69.75 2.48 65 9 HIS A 99 ? ? -90.24 35.87 66 9 ASN A 124 ? ? -60.01 -176.95 67 9 HIS A 125 ? ? -97.56 44.83 68 9 GLU A 127 ? ? 36.22 43.54 69 9 LYS A 128 ? ? -36.55 -33.68 70 9 PRO A 131 ? ? -69.77 1.96 71 9 SER A 132 ? ? -67.91 96.03 72 10 ASP A 9 ? ? -102.87 48.94 73 10 GLU A 57 ? ? -67.02 87.00 74 10 PRO A 91 ? ? -69.84 3.10 75 10 ASN A 124 ? ? -57.97 179.82 76 10 SER A 129 ? ? -94.15 -65.45 77 10 PRO A 131 ? ? -69.77 2.26 78 10 SER A 132 ? ? -35.54 124.11 79 11 ASP A 9 ? ? -90.90 42.82 80 11 THR A 28 ? ? -65.94 -179.06 81 11 GLU A 57 ? ? -55.49 91.15 82 11 PRO A 91 ? ? -69.72 3.26 83 11 HIS A 99 ? ? -85.58 33.68 84 11 ASN A 124 ? ? -49.31 179.73 85 11 HIS A 125 ? ? -97.32 44.67 86 11 SER A 132 ? ? -36.51 104.24 87 12 ARG A 32 ? ? -40.07 -73.72 88 12 GLU A 57 ? ? -66.87 86.80 89 12 MET A 83 ? ? -38.33 115.68 90 12 LEU A 93 ? ? -34.43 -34.55 91 12 HIS A 125 ? ? -110.76 54.22 92 13 ALA A 47 ? ? -52.24 179.08 93 13 PRO A 91 ? ? -69.73 0.89 94 13 LEU A 93 ? ? -38.18 -27.55 95 13 ILE A 122 ? ? -92.42 -62.51 96 13 ASN A 124 ? ? -58.86 -177.93 97 14 SER A 6 ? ? 37.20 45.42 98 14 GLU A 57 ? ? -52.59 96.35 99 14 PRO A 91 ? ? -69.72 4.27 100 14 ASP A 94 ? ? -39.46 130.22 101 14 ILE A 122 ? ? -99.04 -70.66 102 14 HIS A 125 ? ? -114.35 66.18 103 14 GLU A 127 ? ? -64.88 94.51 104 14 LYS A 128 ? ? -169.31 112.62 105 14 PRO A 131 ? ? -69.72 2.76 106 15 SER A 2 ? ? -171.27 145.81 107 15 ASP A 9 ? ? -118.63 70.16 108 15 ALA A 47 ? ? -51.55 171.03 109 15 GLU A 57 ? ? -45.81 96.28 110 15 MET A 83 ? ? -34.52 110.34 111 15 PRO A 91 ? ? -69.79 0.92 112 15 HIS A 99 ? ? -83.70 37.72 113 15 ILE A 122 ? ? -87.29 -72.85 114 15 ASN A 124 ? ? -55.31 -174.79 115 15 HIS A 125 ? ? -93.15 49.15 116 15 VAL A 126 ? ? -115.25 70.49 117 15 SER A 129 ? ? -86.47 -70.69 118 16 SER A 30 ? ? -47.57 -70.17 119 16 ALA A 47 ? ? -53.45 -177.86 120 16 GLU A 57 ? ? -50.29 93.93 121 16 PRO A 91 ? ? -69.75 2.74 122 16 LEU A 93 ? ? -34.93 -36.42 123 16 ASN A 124 ? ? -52.97 -178.82 124 16 GLU A 127 ? ? -34.89 -37.70 125 16 PRO A 131 ? ? -69.75 91.88 126 17 GLU A 16 ? ? -38.87 -36.00 127 17 GLU A 57 ? ? -46.68 99.81 128 17 SER A 60 ? ? -171.64 142.15 129 17 MET A 83 ? ? -36.52 109.94 130 17 PRO A 91 ? ? -69.73 1.37 131 17 LEU A 93 ? ? -35.87 -32.09 132 17 ILE A 122 ? ? -101.97 -69.08 133 18 ASP A 9 ? ? -117.92 74.94 134 18 LEU A 14 ? ? -91.79 -62.01 135 18 GLU A 57 ? ? -58.31 91.78 136 18 MET A 83 ? ? -39.70 110.07 137 18 PRO A 91 ? ? -69.72 0.53 138 18 LEU A 93 ? ? -37.82 -30.37 139 18 ASP A 94 ? ? -48.69 150.53 140 18 HIS A 125 ? ? -115.84 54.04 141 19 ALA A 47 ? ? -52.94 -175.01 142 19 GLU A 57 ? ? -53.05 93.42 143 19 PRO A 91 ? ? -69.78 2.27 144 19 ASN A 124 ? ? -54.99 -175.47 145 19 HIS A 125 ? ? -94.29 55.12 146 19 GLU A 127 ? ? -36.03 103.28 147 20 ALA A 47 ? ? -59.85 170.86 148 20 GLU A 57 ? ? -39.53 106.51 149 20 SER A 60 ? ? -173.16 129.41 150 20 PRO A 91 ? ? -69.75 2.42 151 20 LEU A 123 ? ? -65.54 -70.95 152 20 ASN A 124 ? ? -52.04 -174.96 153 20 HIS A 125 ? ? -110.50 53.16 154 20 SER A 132 ? ? -35.58 121.63 #