data_1MRE # _model_server_result.job_id 3xD0kyg1O4iX6HHIAIlpYw _model_server_result.datetime_utc '2024-11-28 11:14:45' _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 1mre # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":901}' # _entry.id 1MRE # _exptl.entry_id 1MRE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 1MRE _cell.length_a 66.2 _cell.length_b 75.5 _cell.length_c 104.7 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MRE _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 _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 23 L CYS 23 1_555 A SG CYS 93 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 139 L CYS 134 1_555 A SG CYS 199 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf4 B SG CYS 143 H CYS 142 1_555 B SG CYS 198 H CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc1 A OD2 ASP 156 L ASP 151 1_555 C ZN ZN . L ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc2 A ND1 HIS 194 L HIS 189 1_555 C ZN ZN . L ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc3 C ZN ZN . L ZN 600 1_555 D N1 IMD . L IMD 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.7 ? metalc ? metalc4 C ZN ZN . L ZN 600 1_555 B OD2 ASP 210 H ASP 220 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 1MRE _atom_sites.fract_transf_matrix[1][1] 0.015106 _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] 0.013245 _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] 0.009551 _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 C 3 ZN L 1 600 600 ZN ZN . D 4 IMD L 1 902 902 IMD IMD . E 5 GDP L 1 901 901 GDP GDP . F 6 HOH L 1 605 605 HOH HOH . F 6 HOH L 2 606 606 HOH HOH . F 6 HOH L 3 607 607 HOH HOH . F 6 HOH L 4 608 608 HOH HOH . F 6 HOH L 5 611 611 HOH HOH . F 6 HOH L 6 613 613 HOH HOH . F 6 HOH L 7 620 620 HOH HOH . F 6 HOH L 8 621 621 HOH HOH . F 6 HOH L 9 623 623 HOH HOH . F 6 HOH L 10 624 624 HOH HOH . F 6 HOH L 11 627 627 HOH HOH . F 6 HOH L 12 629 629 HOH HOH . F 6 HOH L 13 630 630 HOH HOH . F 6 HOH L 14 631 631 HOH HOH . F 6 HOH L 15 633 633 HOH HOH . F 6 HOH L 16 634 634 HOH HOH . F 6 HOH L 17 635 635 HOH HOH . F 6 HOH L 18 637 637 HOH HOH . F 6 HOH L 19 638 638 HOH HOH . F 6 HOH L 20 642 642 HOH HOH . F 6 HOH L 21 643 643 HOH HOH . F 6 HOH L 22 644 644 HOH HOH . F 6 HOH L 23 645 645 HOH HOH . F 6 HOH L 24 650 650 HOH HOH . F 6 HOH L 25 652 652 HOH HOH . F 6 HOH L 26 654 654 HOH HOH . F 6 HOH L 27 655 655 HOH HOH . F 6 HOH L 28 656 656 HOH HOH . F 6 HOH L 29 658 658 HOH HOH . F 6 HOH L 30 659 659 HOH HOH . F 6 HOH L 31 660 660 HOH HOH . F 6 HOH L 32 661 661 HOH HOH . F 6 HOH L 33 665 665 HOH HOH . F 6 HOH L 34 666 666 HOH HOH . F 6 HOH L 35 668 668 HOH HOH . F 6 HOH L 36 669 669 HOH HOH . F 6 HOH L 37 670 670 HOH HOH . F 6 HOH L 38 671 671 HOH HOH . F 6 HOH L 39 672 672 HOH HOH . F 6 HOH L 40 673 673 HOH HOH . F 6 HOH L 41 674 674 HOH HOH . F 6 HOH L 42 675 675 HOH HOH . G 6 HOH H 1 601 601 HOH HOH . G 6 HOH H 2 602 602 HOH HOH . G 6 HOH H 3 603 603 HOH HOH . G 6 HOH H 4 604 604 HOH HOH . G 6 HOH H 5 609 609 HOH HOH . G 6 HOH H 6 610 610 HOH HOH . G 6 HOH H 7 612 612 HOH HOH . G 6 HOH H 8 614 614 HOH HOH . G 6 HOH H 9 615 615 HOH HOH . G 6 HOH H 10 616 616 HOH HOH . G 6 HOH H 11 617 617 HOH HOH . G 6 HOH H 12 618 618 HOH HOH . G 6 HOH H 13 619 619 HOH HOH . G 6 HOH H 14 622 622 HOH HOH . G 6 HOH H 15 625 625 HOH HOH . G 6 HOH H 16 626 626 HOH HOH . G 6 HOH H 17 628 628 HOH HOH . G 6 HOH H 18 632 632 HOH HOH . G 6 HOH H 19 636 636 HOH HOH . G 6 HOH H 20 639 639 HOH HOH . G 6 HOH H 21 640 640 HOH HOH . G 6 HOH H 22 641 641 HOH HOH . G 6 HOH H 23 646 646 HOH HOH . G 6 HOH H 24 647 647 HOH HOH . G 6 HOH H 25 648 648 HOH HOH . G 6 HOH H 26 649 649 HOH HOH . G 6 HOH H 27 651 651 HOH HOH . G 6 HOH H 28 653 653 HOH HOH . G 6 HOH H 29 657 657 HOH HOH . G 6 HOH H 30 662 662 HOH HOH . G 6 HOH H 31 663 663 HOH HOH . G 6 HOH H 32 664 664 HOH HOH . G 6 HOH H 33 667 667 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 PB GDP . . . E 5 -17.298 15.568 54.941 1 78.55 ? PB GDP 901 L 1 HETATM 2 O O1B GDP . . . E 5 -18.284 14.455 54.89 1 78.09 ? O1B GDP 901 L 1 HETATM 3 O O2B GDP . . . E 5 -17.909 16.915 54.879 1 78.24 ? O2B GDP 901 L 1 HETATM 4 O O3B GDP . . . E 5 -16.269 15.417 56.007 1 77.89 ? O3B GDP 901 L 1 HETATM 5 O O3A GDP . . . E 5 -16.451 15.409 53.558 1 73.08 ? O3A GDP 901 L 1 HETATM 6 P PA GDP . . . E 5 -16.61 15.966 52.055 1 62.65 ? PA GDP 901 L 1 HETATM 7 O O1A GDP . . . E 5 -15.547 15.413 51.184 1 65.21 ? O1A GDP 901 L 1 HETATM 8 O O2A GDP . . . E 5 -16.791 17.433 52.109 1 65.66 ? O2A GDP 901 L 1 HETATM 9 O O5' GDP . . . E 5 -17.968 15.287 51.557 1 59.99 ? O5' GDP 901 L 1 HETATM 10 C C5' GDP . . . E 5 -19.253 15.84 51.878 1 53.72 ? C5' GDP 901 L 1 HETATM 11 C C4' GDP . . . E 5 -20.004 16.118 50.589 1 50.93 ? C4' GDP 901 L 1 HETATM 12 O O4' GDP . . . E 5 -19.506 17.182 49.778 1 48.43 ? O4' GDP 901 L 1 HETATM 13 C C3' GDP . . . E 5 -20.292 15.05 49.557 1 50.67 ? C3' GDP 901 L 1 HETATM 14 O O3' GDP . . . E 5 -21.351 15.445 48.696 1 58.02 ? O3' GDP 901 L 1 HETATM 15 C C2' GDP . . . E 5 -18.993 15.042 48.799 1 48.06 ? C2' GDP 901 L 1 HETATM 16 O O2' GDP . . . E 5 -19.024 14.35 47.562 1 50.26 ? O2' GDP 901 L 1 HETATM 17 C C1' GDP . . . E 5 -18.821 16.541 48.702 1 44.21 ? C1' GDP 901 L 1 HETATM 18 N N9 GDP . . . E 5 -17.534 17.092 48.316 1 39.73 ? N9 GDP 901 L 1 HETATM 19 C C8 GDP . . . E 5 -16.336 16.517 48.451 1 37.69 ? C8 GDP 901 L 1 HETATM 20 N N7 GDP . . . E 5 -15.4 17.336 47.979 1 37.93 ? N7 GDP 901 L 1 HETATM 21 C C5 GDP . . . E 5 -16.034 18.437 47.556 1 33.87 ? C5 GDP 901 L 1 HETATM 22 C C6 GDP . . . E 5 -15.493 19.774 47.049 1 25.97 ? C6 GDP 901 L 1 HETATM 23 O O6 GDP . . . E 5 -14.339 20.16 46.91 1 22.39 ? O6 GDP 901 L 1 HETATM 24 N N1 GDP . . . E 5 -16.532 20.587 46.676 1 27.37 ? N1 GDP 901 L 1 HETATM 25 C C2 GDP . . . E 5 -17.878 20.256 46.726 1 27.11 ? C2 GDP 901 L 1 HETATM 26 N N2 GDP . . . E 5 -18.743 21.145 46.235 1 21.98 ? N2 GDP 901 L 1 HETATM 27 N N3 GDP . . . E 5 -18.346 19.117 47.276 1 30.92 ? N3 GDP 901 L 1 HETATM 28 C C4 GDP . . . E 5 -17.409 18.263 47.729 1 34.44 ? C4 GDP 901 L 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #