data_5MZA # _model_server_result.job_id yXF3l8zJcEtpTyG8HPkUpg _model_server_result.datetime_utc '2024-12-04 12:49:16' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5mza # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1301}' # _entry.id 5MZA # _exptl.entry_id 5MZA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 257.955 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description TRIPHOSPHATE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5MZA _cell.length_a 68.639 _cell.length_b 109.83 _cell.length_c 112.83 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MZA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG B 211 NAG 3 n C NAG 2 C 2 NAG B 212 NAG # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 4 A CYS 730 1_555 A SG CYS 456 A CYS 1182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 62 A CYS 788 1_555 A SG CYS 251 A CYS 977 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 79 A CYS 805 1_555 A SG CYS 117 A CYS 843 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 173 A CYS 899 1_555 A SG CYS 257 A CYS 983 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 285 A CYS 1011 1_555 A SG CYS 449 A CYS 1175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 A SG CYS 298 A CYS 1024 1_555 A SG CYS 318 A CYS 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 315 A CYS 1041 1_555 A SG CYS 488 A CYS 1214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 A SG CYS 322 A CYS 1048 1_555 A SG CYS 486 A CYS 1212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 21 B CYS 21 1_555 B SG CYS 65 B CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 B SG CYS 25 B CYS 25 1_555 B SG CYS 69 B CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 B SG CYS 108 B CYS 108 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 B ND2 ASN 118 B ASN 118 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 B ND2 ASN 156 B ASN 156 1_555 F C1 NAG . B NAG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 B ND2 ASN 175 B ASN 175 1_555 E C1 NAG . B NAG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? # _chem_comp.formula 'H5 O10 P3' _chem_comp.formula_weight 257.955 _chem_comp.id 3PO _chem_comp.mon_nstd_flag . _chem_comp.name TRIPHOSPHATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PG O1G 3PO doub 1 n n PG O2G 3PO sing 2 n n PG O3G 3PO sing 3 n n PG O3B 3PO sing 4 n n O2G HOG2 3PO sing 5 n n O3G HOG3 3PO sing 6 n n PB O1B 3PO doub 7 n n PB O2B 3PO sing 8 n n PB O3B 3PO sing 9 n n PB O3A 3PO sing 10 n n O2B HOB2 3PO sing 11 n n PA O1A 3PO doub 12 n n PA O2A 3PO sing 13 n n PA O3A 3PO sing 14 n n PA O5' 3PO sing 15 n n O2A HOA2 3PO sing 16 n n O5' HO5' 3PO sing 17 n n # _atom_sites.entry_id 5MZA _atom_sites.fract_transf_matrix[1][1] 0.014569 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009105 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008863 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 3PO A 1 1301 15 3PO 3PO . E 5 NAG B 1 203 221 NAG NAG . F 5 NAG B 1 204 231 NAG NAG . G 6 IHP B 1 205 14 IHP IHP . H 7 HOH A 1 1401 5 HOH HOH . H 7 HOH A 2 1402 1 HOH HOH . H 7 HOH A 3 1403 2 HOH HOH . H 7 HOH A 4 1404 9 HOH HOH . H 7 HOH A 5 1405 6 HOH HOH . H 7 HOH A 6 1406 3 HOH HOH . H 7 HOH A 7 1407 4 HOH HOH . I 7 HOH B 1 301 10 HOH HOH . I 7 HOH B 2 302 12 HOH HOH . I 7 HOH B 3 303 13 HOH HOH . I 7 HOH B 4 304 11 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PG 3PO . . . D 4 -21.804 0.467 61.673 1 156.68 ? PG 3PO 1301 A 1 HETATM 2 O O1G 3PO . . . D 4 -22.69 0.131 60.469 1 156.02 ? O1G 3PO 1301 A 1 HETATM 3 O O2G 3PO . . . D 4 -20.878 -0.723 61.928 1 156.52 ? O2G 3PO 1301 A 1 HETATM 4 O O3G 3PO . . . D 4 -22.582 0.867 62.886 1 157.81 ? O3G 3PO 1301 A 1 HETATM 5 P PB 3PO . . . D 4 -20.602 2.361 59.804 1 154.82 ? PB 3PO 1301 A 1 HETATM 6 O O1B 3PO . . . D 4 -21.863 2.367 59.042 1 154.78 ? O1B 3PO 1301 A 1 HETATM 7 O O2B 3PO . . . D 4 -19.545 1.554 59.055 1 153.84 ? O2B 3PO 1301 A 1 HETATM 8 O O3B 3PO . . . D 4 -20.86 1.665 61.213 1 156.11 ? O3B 3PO 1301 A 1 HETATM 9 P PA 3PO . . . D 4 -20.68 5.197 60.555 1 156.35 ? PA 3PO 1301 A 1 HETATM 10 O O1A 3PO . . . D 4 -20.659 6.189 59.389 1 156.02 ? O1A 3PO 1301 A 1 HETATM 11 O O2A 3PO . . . D 4 -19.704 5.697 61.626 1 156.95 ? O2A 3PO 1301 A 1 HETATM 12 O O3A 3PO . . . D 4 -20.053 3.846 59.988 1 155.13 ? O3A 3PO 1301 A 1 HETATM 13 O O5' 3PO . . . D 4 -22.054 4.961 61.094 1 157.11 ? O5' 3PO 1301 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 13 #