data_2DAK # _entry.id 2DAK # _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 2DAK pdb_00002dak 10.2210/pdb2dak/pdb RCSB RCSB025187 ? ? WWPDB D_1000025187 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id hsi002005673.2 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2DAK _pdbx_database_status.recvd_initial_deposition_date 2005-12-14 _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 'Zhao, C.' 1 'Kigawa, T.' 2 'Sato, M.' 3 'Koshiba, S.' 4 'Inoue, M.' 5 'Yokoyama, S.' 6 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 7 # _citation.id primary _citation.title 'Solution Structure of the Second UBA Domain in the Human Ubiquitin Specific Protease 5 (Isopeptidase 5)' _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 'Zhao, C.' 1 ? primary 'Kigawa, T.' 2 ? primary 'Sato, M.' 3 ? primary 'Koshiba, S.' 4 ? primary 'Inoue, M.' 5 ? primary 'Yokoyama, S.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'Ubiquitin carboxyl-terminal hydrolase 5' _entity.formula_weight 6519.079 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec 3.1.2.15 _entity.pdbx_mutation ? _entity.pdbx_fragment 'UBA domain' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Ubiquitin thiolesterase 5, Ubiquitin-specific processing protease 5, Deubiquitinating enzyme 5, Isopeptidase T' # _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 GSSGSSGPPEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDDLDAEAAMSGPSSG _entity_poly.pdbx_seq_one_letter_code_can GSSGSSGPPEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDDLDAEAAMSGPSSG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier hsi002005673.2 # 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 PRO n 1 9 PRO n 1 10 GLU n 1 11 ASP n 1 12 CYS n 1 13 VAL n 1 14 THR n 1 15 THR n 1 16 ILE n 1 17 VAL n 1 18 SER n 1 19 MET n 1 20 GLY n 1 21 PHE n 1 22 SER n 1 23 ARG n 1 24 ASP n 1 25 GLN n 1 26 ALA n 1 27 LEU n 1 28 LYS n 1 29 ALA n 1 30 LEU n 1 31 ARG n 1 32 ALA n 1 33 THR n 1 34 ASN n 1 35 ASN n 1 36 SER n 1 37 LEU n 1 38 GLU n 1 39 ARG n 1 40 ALA n 1 41 VAL n 1 42 ASP n 1 43 TRP n 1 44 ILE n 1 45 PHE n 1 46 SER n 1 47 HIS n 1 48 ILE n 1 49 ASP n 1 50 ASP n 1 51 LEU n 1 52 ASP n 1 53 ALA n 1 54 GLU n 1 55 ALA n 1 56 ALA n 1 57 MET n 1 58 SER n 1 59 GLY n 1 60 PRO n 1 61 SER n 1 62 SER n 1 63 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 USP5 _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 P050704-16 _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 UBP5_HUMAN _struct_ref.pdbx_db_accession P45974 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 723 _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 2DAK _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 57 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P45974 _struct_ref_seq.db_align_beg 723 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 772 _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 57 # 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 2DAK GLY A 1 ? UNP P45974 ? ? 'cloning artifact' 1 1 1 2DAK SER A 2 ? UNP P45974 ? ? 'cloning artifact' 2 2 1 2DAK SER A 3 ? UNP P45974 ? ? 'cloning artifact' 3 3 1 2DAK GLY A 4 ? UNP P45974 ? ? 'cloning artifact' 4 4 1 2DAK SER A 5 ? UNP P45974 ? ? 'cloning artifact' 5 5 1 2DAK SER A 6 ? UNP P45974 ? ? 'cloning artifact' 6 6 1 2DAK GLY A 7 ? UNP P45974 ? ? 'cloning artifact' 7 7 1 2DAK SER A 58 ? UNP P45974 ? ? 'cloning artifact' 58 8 1 2DAK GLY A 59 ? UNP P45974 ? ? 'cloning artifact' 59 9 1 2DAK PRO A 60 ? UNP P45974 ? ? 'cloning artifact' 60 10 1 2DAK SER A 61 ? UNP P45974 ? ? 'cloning artifact' 61 11 1 2DAK SER A 62 ? UNP P45974 ? ? 'cloning artifact' 62 12 1 2DAK GLY A 63 ? UNP P45974 ? ? 'cloning artifact' 63 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 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 296.0 _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 '0.84mM UBA domain U-15N, 13C; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 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 700 _pdbx_nmr_spectrometer.type ? # _pdbx_nmr_refine.entry_id 2DAK _pdbx_nmr_refine.method 'torsion angle dynamics, restrainted molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 2DAK _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 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 2DAK _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 Bruker' 1 processing NMRPipe 20030801 'Delaglio, F.' 2 'data analysis' NMRView 5.0.4 'Johnson, B. A.' 3 'data analysis' KUJIRA 0.9321 'Kobayashi, N.' 4 'structure solution' CYANA 1.0.8 'Guntert, P.' 5 refinement CYANA 1.0.8 'Guntert, P.' 6 # _exptl.entry_id 2DAK _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2DAK _struct.title 'Solution Structure of the Second UBA Domain in the Human Ubiquitin Specific Protease 5 (Isopeptidase 5)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2DAK _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text ;isopeptidase T, Ubiquitin Specific Protease 5, USP 5, UBA domain, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, HYDROLASE ; # _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 PRO A 9 ? GLY A 20 ? PRO A 9 GLY A 20 1 ? 12 HELX_P HELX_P2 2 SER A 22 ? THR A 33 ? SER A 22 THR A 33 1 ? 12 HELX_P HELX_P3 3 LEU A 37 ? ASP A 50 ? LEU A 37 ASP A 50 1 ? 14 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _database_PDB_matrix.entry_id 2DAK _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 2DAK _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 PRO 8 8 8 PRO PRO A . n A 1 9 PRO 9 9 9 PRO PRO A . n A 1 10 GLU 10 10 10 GLU GLU A . n A 1 11 ASP 11 11 11 ASP ASP A . n A 1 12 CYS 12 12 12 CYS CYS A . n A 1 13 VAL 13 13 13 VAL VAL A . n A 1 14 THR 14 14 14 THR THR A . n A 1 15 THR 15 15 15 THR THR A . n A 1 16 ILE 16 16 16 ILE ILE A . n A 1 17 VAL 17 17 17 VAL VAL A . n A 1 18 SER 18 18 18 SER SER A . n A 1 19 MET 19 19 19 MET MET A . n A 1 20 GLY 20 20 20 GLY GLY A . n A 1 21 PHE 21 21 21 PHE PHE A . n A 1 22 SER 22 22 22 SER SER A . n A 1 23 ARG 23 23 23 ARG ARG A . n A 1 24 ASP 24 24 24 ASP ASP A . n A 1 25 GLN 25 25 25 GLN GLN A . n A 1 26 ALA 26 26 26 ALA ALA A . n A 1 27 LEU 27 27 27 LEU LEU A . n A 1 28 LYS 28 28 28 LYS LYS A . n A 1 29 ALA 29 29 29 ALA ALA A . n A 1 30 LEU 30 30 30 LEU LEU A . n A 1 31 ARG 31 31 31 ARG ARG A . n A 1 32 ALA 32 32 32 ALA ALA A . n A 1 33 THR 33 33 33 THR THR A . n A 1 34 ASN 34 34 34 ASN ASN A . n A 1 35 ASN 35 35 35 ASN ASN A . n A 1 36 SER 36 36 36 SER SER A . n A 1 37 LEU 37 37 37 LEU LEU A . n A 1 38 GLU 38 38 38 GLU GLU A . n A 1 39 ARG 39 39 39 ARG ARG A . n A 1 40 ALA 40 40 40 ALA ALA A . n A 1 41 VAL 41 41 41 VAL VAL A . n A 1 42 ASP 42 42 42 ASP ASP A . n A 1 43 TRP 43 43 43 TRP TRP A . n A 1 44 ILE 44 44 44 ILE ILE A . n A 1 45 PHE 45 45 45 PHE PHE A . n A 1 46 SER 46 46 46 SER SER A . n A 1 47 HIS 47 47 47 HIS HIS A . n A 1 48 ILE 48 48 48 ILE ILE A . n A 1 49 ASP 49 49 49 ASP ASP A . n A 1 50 ASP 50 50 50 ASP ASP A . n A 1 51 LEU 51 51 51 LEU LEU A . n A 1 52 ASP 52 52 52 ASP ASP A . n A 1 53 ALA 53 53 53 ALA ALA A . n A 1 54 GLU 54 54 54 GLU GLU A . n A 1 55 ALA 55 55 55 ALA ALA A . n A 1 56 ALA 56 56 56 ALA ALA A . n A 1 57 MET 57 57 57 MET MET A . n A 1 58 SER 58 58 58 SER SER A . n A 1 59 GLY 59 59 59 GLY GLY A . n A 1 60 PRO 60 60 60 PRO PRO A . n A 1 61 SER 61 61 61 SER SER A . n A 1 62 SER 62 62 62 SER SER A . n A 1 63 GLY 63 63 63 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 2006-06-14 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_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 1 O A THR 14 ? ? H A SER 18 ? ? 1.54 2 1 O A GLN 25 ? ? H A ALA 29 ? ? 1.54 3 1 O A ARG 39 ? ? H A TRP 43 ? ? 1.56 4 2 O A THR 14 ? ? H A SER 18 ? ? 1.52 5 3 O A THR 14 ? ? H A SER 18 ? ? 1.51 6 3 O A GLN 25 ? ? H A ALA 29 ? ? 1.55 7 3 O A LEU 30 ? ? H A ASN 35 ? ? 1.58 8 4 O A THR 14 ? ? H A SER 18 ? ? 1.50 9 4 O A GLU 10 ? ? H A THR 14 ? ? 1.52 10 4 O A GLN 25 ? ? H A ALA 29 ? ? 1.55 11 4 O A LEU 30 ? ? H A ASN 35 ? ? 1.56 12 4 O A ARG 39 ? ? H A TRP 43 ? ? 1.57 13 4 O A LYS 28 ? ? H A ALA 32 ? ? 1.58 14 5 O A THR 14 ? ? H A SER 18 ? ? 1.51 15 5 O A GLN 25 ? ? H A ALA 29 ? ? 1.55 16 5 O A ARG 39 ? ? H A TRP 43 ? ? 1.56 17 6 O A THR 14 ? ? H A SER 18 ? ? 1.51 18 6 O A GLN 25 ? ? H A ALA 29 ? ? 1.56 19 6 O A ARG 39 ? ? H A TRP 43 ? ? 1.57 20 6 O A LYS 28 ? ? H A ALA 32 ? ? 1.58 21 7 O A THR 14 ? ? H A SER 18 ? ? 1.50 22 7 O A ASP 24 ? ? H A LYS 28 ? ? 1.52 23 7 O A ARG 39 ? ? H A TRP 43 ? ? 1.54 24 7 O A GLU 10 ? ? H A THR 14 ? ? 1.54 25 7 O A GLN 25 ? ? H A ALA 29 ? ? 1.58 26 7 O A LEU 30 ? ? H A ASN 35 ? ? 1.58 27 7 O A SER 36 ? ? H A ALA 40 ? ? 1.59 28 8 O A GLN 25 ? ? H A ALA 29 ? ? 1.54 29 8 O A ALA 29 ? ? H A THR 33 ? ? 1.58 30 9 O A THR 14 ? ? H A SER 18 ? ? 1.50 31 9 O A ALA 29 ? ? H A THR 33 ? ? 1.56 32 9 O A LYS 28 ? ? H A ALA 32 ? ? 1.57 33 9 O A ALA 40 ? ? H A ILE 44 ? ? 1.58 34 9 O A GLN 25 ? ? H A ALA 29 ? ? 1.59 35 10 O A GLN 25 ? ? H A ALA 29 ? ? 1.53 36 10 O A THR 14 ? ? H A SER 18 ? ? 1.57 37 10 O A ALA 29 ? ? H A THR 33 ? ? 1.57 38 11 O A THR 14 ? ? H A SER 18 ? ? 1.50 39 11 O A GLN 25 ? ? H A ALA 29 ? ? 1.51 40 11 O A ALA 29 ? ? H A THR 33 ? ? 1.57 41 12 O A THR 14 ? ? H A SER 18 ? ? 1.51 42 12 O A ARG 39 ? ? H A TRP 43 ? ? 1.53 43 12 O A LEU 30 ? ? H A THR 33 ? ? 1.56 44 12 O A ASP 24 ? ? H A LYS 28 ? ? 1.57 45 12 O A LEU 30 ? ? H A ASN 35 ? ? 1.58 46 12 O A GLN 25 ? ? H A ALA 29 ? ? 1.60 47 13 O A THR 14 ? ? H A SER 18 ? ? 1.54 48 13 O A GLU 10 ? ? H A THR 14 ? ? 1.55 49 13 O A ALA 40 ? ? H A ILE 44 ? ? 1.55 50 13 O A ALA 29 ? ? H A THR 33 ? ? 1.56 51 13 O A GLN 25 ? ? H A ALA 29 ? ? 1.58 52 14 O A THR 14 ? ? H A SER 18 ? ? 1.50 53 14 O A GLN 25 ? ? H A ALA 29 ? ? 1.55 54 14 O A ALA 29 ? ? H A THR 33 ? ? 1.57 55 15 O A GLU 10 ? ? H A THR 14 ? ? 1.51 56 15 O A GLN 25 ? ? H A ALA 29 ? ? 1.53 57 15 O A THR 14 ? ? H A SER 18 ? ? 1.53 58 15 O A ALA 29 ? ? H A THR 33 ? ? 1.56 59 15 O A SER 36 ? ? H A ALA 40 ? ? 1.59 60 15 O A LYS 28 ? ? H A ALA 32 ? ? 1.59 61 16 O A THR 14 ? ? H A SER 18 ? ? 1.50 62 16 O A GLN 25 ? ? H A ALA 29 ? ? 1.55 63 16 O A ALA 29 ? ? H A THR 33 ? ? 1.60 64 17 O A ASP 24 ? ? H A LYS 28 ? ? 1.50 65 17 O A THR 14 ? ? H A SER 18 ? ? 1.54 66 17 O A ARG 39 ? ? H A TRP 43 ? ? 1.55 67 17 O A LEU 30 ? ? H A ASN 35 ? ? 1.57 68 17 O A GLN 25 ? ? H A ALA 29 ? ? 1.58 69 18 O A THR 14 ? ? H A SER 18 ? ? 1.50 70 18 O A GLN 25 ? ? H A ALA 29 ? ? 1.54 71 18 O A LEU 30 ? ? H A ASN 35 ? ? 1.56 72 18 O A SER 36 ? ? H A ALA 40 ? ? 1.56 73 19 O A THR 14 ? ? H A SER 18 ? ? 1.50 74 19 O A LEU 30 ? ? H A ASN 35 ? ? 1.54 75 19 O A ARG 39 ? ? H A TRP 43 ? ? 1.55 76 19 O A GLN 25 ? ? H A ALA 29 ? ? 1.55 77 19 O A SER 36 ? ? H A ALA 40 ? ? 1.55 78 20 O A GLN 25 ? ? H A ALA 29 ? ? 1.53 79 20 O A THR 14 ? ? H A SER 18 ? ? 1.54 80 20 O A ASP 24 ? ? H A LYS 28 ? ? 1.57 81 20 O A ALA 29 ? ? H A THR 33 ? ? 1.58 82 20 O A ASP 11 ? ? H A THR 15 ? ? 1.59 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 SER A 3 ? ? -178.16 88.46 2 1 SER A 6 ? ? -47.79 160.22 3 1 ASP A 50 ? ? 168.44 -38.01 4 1 LEU A 51 ? ? -67.73 78.76 5 1 GLU A 54 ? ? -41.63 157.48 6 1 SER A 61 ? ? -178.93 123.71 7 2 SER A 5 ? ? -179.94 -59.31 8 2 SER A 6 ? ? -152.00 83.02 9 2 ASN A 35 ? ? 48.97 70.56 10 2 ASP A 52 ? ? -140.11 -55.52 11 2 ALA A 53 ? ? 51.17 73.22 12 2 ALA A 56 ? ? -164.15 88.10 13 3 SER A 3 ? ? 62.97 111.90 14 3 SER A 6 ? ? 58.31 102.22 15 3 THR A 33 ? ? -102.30 45.35 16 3 ASN A 35 ? ? 65.17 69.87 17 3 ASP A 50 ? ? -116.44 77.18 18 3 ALA A 53 ? ? -177.63 80.38 19 3 GLU A 54 ? ? 73.64 -58.61 20 3 ALA A 55 ? ? 51.31 97.71 21 3 ALA A 56 ? ? -161.56 112.50 22 3 MET A 57 ? ? 58.44 87.30 23 4 SER A 5 ? ? -67.02 79.46 24 4 THR A 33 ? ? -88.99 40.16 25 4 ASN A 35 ? ? 65.61 82.63 26 4 ASP A 50 ? ? 179.89 106.96 27 4 GLU A 54 ? ? -165.18 113.45 28 4 SER A 61 ? ? -42.83 163.39 29 4 SER A 62 ? ? 48.03 92.12 30 5 ASN A 35 ? ? 61.49 66.66 31 5 ASP A 50 ? ? 60.40 103.33 32 5 ALA A 55 ? ? 51.25 97.37 33 5 ALA A 56 ? ? -64.91 91.86 34 5 SER A 61 ? ? 56.48 108.00 35 5 SER A 62 ? ? 178.36 147.67 36 6 SER A 5 ? ? -123.10 -58.51 37 6 THR A 33 ? ? -97.43 43.02 38 6 ILE A 44 ? ? -72.47 -70.98 39 6 ASP A 50 ? ? 65.63 107.28 40 6 ASP A 52 ? ? 49.45 94.00 41 6 ALA A 53 ? ? -161.77 63.26 42 6 GLU A 54 ? ? 58.07 80.13 43 6 SER A 58 ? ? 70.07 -62.80 44 6 SER A 62 ? ? 59.74 152.41 45 7 SER A 3 ? ? -148.01 -59.45 46 7 SER A 6 ? ? 59.73 152.56 47 7 ASN A 35 ? ? 61.69 79.92 48 7 ASP A 49 ? ? -169.89 96.86 49 7 ASP A 52 ? ? 60.18 109.00 50 7 SER A 61 ? ? -171.04 117.46 51 8 SER A 3 ? ? -160.41 -58.59 52 8 SER A 5 ? ? -122.68 -57.90 53 8 THR A 33 ? ? -89.03 40.19 54 8 ASN A 35 ? ? 58.38 71.51 55 8 ALA A 53 ? ? -131.98 -46.28 56 8 GLU A 54 ? ? -173.06 81.84 57 8 ALA A 55 ? ? -166.50 -59.19 58 9 SER A 3 ? ? -162.16 99.94 59 9 SER A 5 ? ? -156.76 76.88 60 9 SER A 6 ? ? -143.05 -60.96 61 9 ILE A 16 ? ? -54.31 -71.71 62 9 THR A 33 ? ? -89.02 40.16 63 9 ASN A 35 ? ? 40.46 80.02 64 9 ILE A 44 ? ? -54.46 -71.81 65 9 LEU A 51 ? ? -67.32 75.57 66 9 ASP A 52 ? ? 71.33 112.02 67 9 ALA A 53 ? ? -175.15 74.27 68 9 GLU A 54 ? ? -39.24 111.70 69 9 ALA A 55 ? ? -169.81 81.21 70 9 MET A 57 ? ? -157.79 88.09 71 10 SER A 3 ? ? 62.60 140.15 72 10 SER A 5 ? ? -150.57 -60.05 73 10 SER A 6 ? ? 60.70 161.87 74 10 THR A 33 ? ? -93.89 42.42 75 10 ASN A 35 ? ? 40.59 73.23 76 10 ILE A 44 ? ? -56.57 -70.13 77 10 ASP A 50 ? ? 60.94 103.71 78 10 ASP A 52 ? ? -161.79 102.04 79 10 ALA A 53 ? ? -158.85 74.64 80 10 ALA A 55 ? ? -160.76 99.05 81 10 ALA A 56 ? ? 46.75 78.46 82 10 MET A 57 ? ? -169.62 107.23 83 11 SER A 3 ? ? -39.95 141.29 84 11 SER A 5 ? ? 53.28 83.40 85 11 SER A 6 ? ? 60.53 86.18 86 11 GLU A 10 ? ? -90.40 -61.63 87 11 ILE A 16 ? ? -54.71 -71.71 88 11 ASN A 35 ? ? 40.45 76.68 89 11 ILE A 44 ? ? -63.93 -70.06 90 11 ASP A 52 ? ? 55.04 97.73 91 11 ALA A 53 ? ? -156.04 -45.87 92 11 GLU A 54 ? ? 65.47 155.25 93 11 ALA A 55 ? ? 62.51 77.40 94 12 SER A 5 ? ? -150.42 -61.47 95 12 SER A 6 ? ? 66.06 96.58 96 12 ASN A 34 ? ? 56.00 19.18 97 12 ASN A 35 ? ? 79.78 62.92 98 12 ILE A 44 ? ? -71.01 -72.33 99 12 ASP A 50 ? ? 173.17 113.19 100 12 ASP A 52 ? ? -124.53 -57.49 101 12 GLU A 54 ? ? -156.80 -59.87 102 12 ALA A 55 ? ? 64.19 153.22 103 12 ALA A 56 ? ? 42.47 79.15 104 12 SER A 61 ? ? -157.57 88.49 105 12 SER A 62 ? ? 57.64 83.93 106 13 SER A 2 ? ? 49.30 95.53 107 13 GLU A 10 ? ? -90.16 -62.90 108 13 THR A 33 ? ? -90.96 32.70 109 13 ASN A 35 ? ? 42.45 79.41 110 13 ILE A 44 ? ? -56.10 -70.10 111 13 ASP A 50 ? ? 67.07 110.23 112 13 LEU A 51 ? ? -104.17 -63.97 113 13 ALA A 53 ? ? -161.77 -44.45 114 13 ALA A 55 ? ? 48.30 83.66 115 13 MET A 57 ? ? 56.99 109.65 116 13 SER A 62 ? ? -175.02 126.54 117 14 SER A 2 ? ? 57.30 92.47 118 14 SER A 3 ? ? 57.89 96.07 119 14 ILE A 16 ? ? -57.18 -71.35 120 14 THR A 33 ? ? -93.79 42.42 121 14 ASP A 50 ? ? -138.70 -47.25 122 14 ASP A 52 ? ? 42.70 86.83 123 14 GLU A 54 ? ? 68.79 148.63 124 14 ALA A 55 ? ? -64.71 88.83 125 14 ALA A 56 ? ? -166.40 62.05 126 15 SER A 2 ? ? 62.64 159.18 127 15 SER A 3 ? ? -174.19 -58.50 128 15 ASN A 34 ? ? 44.12 73.12 129 15 ASN A 35 ? ? 40.47 83.44 130 15 ASP A 50 ? ? -160.62 99.94 131 15 ASP A 52 ? ? 55.15 101.52 132 15 ALA A 56 ? ? -173.88 102.24 133 15 SER A 62 ? ? -43.55 107.80 134 16 SER A 2 ? ? -162.06 110.22 135 16 SER A 6 ? ? -142.39 -59.63 136 16 CYS A 12 ? ? -50.24 -70.01 137 16 THR A 33 ? ? -97.36 44.31 138 16 ILE A 44 ? ? -64.80 -70.64 139 16 ASP A 49 ? ? -100.01 69.82 140 16 ASP A 50 ? ? -169.58 69.55 141 16 LEU A 51 ? ? 38.33 87.21 142 16 ASP A 52 ? ? -171.67 92.37 143 16 GLU A 54 ? ? -107.88 53.45 144 16 ALA A 56 ? ? -58.14 171.83 145 16 SER A 62 ? ? -170.65 82.49 146 17 SER A 2 ? ? 179.61 145.46 147 17 ASN A 34 ? ? 40.49 29.90 148 17 ASN A 35 ? ? 70.11 66.57 149 17 HIS A 47 ? ? -90.79 45.47 150 17 ASP A 49 ? ? 70.26 -61.02 151 17 ASP A 50 ? ? 178.37 100.88 152 17 ASP A 52 ? ? -152.02 -56.29 153 17 ALA A 55 ? ? -133.17 -62.00 154 17 ALA A 56 ? ? 58.94 78.67 155 17 SER A 62 ? ? 63.13 106.92 156 18 ILE A 16 ? ? -59.33 -72.41 157 18 THR A 33 ? ? -95.51 43.03 158 18 ASN A 35 ? ? 67.89 71.10 159 18 ILE A 44 ? ? -62.67 -71.26 160 18 LEU A 51 ? ? -102.29 69.30 161 18 ASP A 52 ? ? -179.06 128.36 162 18 GLU A 54 ? ? 48.75 97.30 163 18 ALA A 56 ? ? 63.18 106.31 164 19 SER A 3 ? ? 67.17 -72.34 165 19 SER A 6 ? ? 65.94 153.06 166 19 THR A 33 ? ? -89.81 39.39 167 19 ASN A 35 ? ? 67.72 70.55 168 19 HIS A 47 ? ? -91.58 43.76 169 19 ASP A 52 ? ? 44.66 91.27 170 20 SER A 3 ? ? -176.50 128.74 171 20 SER A 5 ? ? 64.38 88.61 172 20 SER A 6 ? ? -155.70 -58.63 173 20 THR A 33 ? ? -96.21 43.61 174 20 ASN A 35 ? ? 40.21 70.71 175 20 LEU A 51 ? ? 38.36 78.82 176 20 ASP A 52 ? ? 174.44 118.90 177 20 ALA A 55 ? ? 61.66 168.82 #