data_1MRF # _model_server_result.job_id '_flZykJ9CpjCp0JTI5z85A' _model_server_result.datetime_utc '2024-11-28 10:40:28' _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 1mrf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":901}' # _entry.id 1MRF # _exptl.entry_id 1MRF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 332.207 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYINOSINE-5'-MONOPHOSPHATE" _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 1MRF _cell.length_a 66.2 _cell.length_b 75.5 _cell.length_c 104.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MRF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,C,D,E,F 2 1 B,G 2 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_655 -x+1,y+1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 66.2 37.75 52.3 # _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf2 A SG CYS 139 L CYS 134 1_555 A SG CYS 199 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf4 B SG CYS 143 H CYS 142 1_555 B SG CYS 198 H CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc1 A OD2 ASP 156 L ASP 151 1_555 C ZN ZN . L ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc2 A ND1 HIS 194 L HIS 189 1_555 C ZN ZN . L ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc3 C ZN ZN . L ZN 600 1_555 D N1 IMD . L IMD 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? metalc ? metalc4 C ZN ZN . L ZN 600 1_555 B OD2 ASP 210 H ASP 220 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 1.805 ? # _chem_comp.formula 'C10 H13 N4 O7 P' _chem_comp.formula_weight 332.207 _chem_comp.id DI _chem_comp.mon_nstd_flag y _chem_comp.name "2'-DEOXYINOSINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna 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 OP3 P DI sing 83 n n OP3 HOP3 DI sing 84 n n P OP1 DI doub 85 n n P OP2 DI sing 86 n n P O5' DI sing 87 n n OP2 HOP2 DI sing 88 n n O5' C5' DI sing 89 n n C5' C4' DI sing 90 n n C5' H5' DI sing 91 n n C5' "H5''" DI sing 92 n n C4' O4' DI sing 93 n n C4' C3' DI sing 94 n n C4' H4' DI sing 95 n n O4' C1' DI sing 96 n n C3' O3' DI sing 97 n n C3' C2' DI sing 98 n n C3' H3' DI sing 99 n n O3' HO3' DI sing 100 n n C2' C1' DI sing 101 n n C2' H2' DI sing 102 n n C2' "H2''" DI sing 103 n n C1' N9 DI sing 104 n n C1' H1' DI sing 105 n n N9 C8 DI sing 106 n y N9 C4 DI sing 107 n y C8 N7 DI doub 108 n y C8 H8 DI sing 109 n n N7 C5 DI sing 110 n y C5 C6 DI sing 111 n n C5 C4 DI doub 112 n y C6 O6 DI doub 113 n n C6 N1 DI sing 114 n n N1 C2 DI sing 115 n n N1 H1 DI sing 116 n n C2 N3 DI doub 117 n n C2 H2 DI sing 118 n n N3 C4 DI sing 119 n n # _atom_sites.entry_id 1MRF _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] 0.00956 _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 DI L 1 901 901 DI OIP . F 6 HOH L 1 607 607 HOH HOH . F 6 HOH L 2 608 608 HOH HOH . F 6 HOH L 3 609 609 HOH HOH . F 6 HOH L 4 610 610 HOH HOH . F 6 HOH L 5 612 612 HOH HOH . F 6 HOH L 6 613 613 HOH HOH . F 6 HOH L 7 614 614 HOH HOH . F 6 HOH L 8 616 616 HOH HOH . F 6 HOH L 9 620 620 HOH HOH . F 6 HOH L 10 621 621 HOH HOH . F 6 HOH L 11 623 623 HOH HOH . F 6 HOH L 12 625 625 HOH HOH . F 6 HOH L 13 627 627 HOH HOH . F 6 HOH L 14 630 630 HOH HOH . F 6 HOH L 15 635 635 HOH HOH . F 6 HOH L 16 636 636 HOH HOH . F 6 HOH L 17 639 639 HOH HOH . F 6 HOH L 18 640 640 HOH HOH . F 6 HOH L 19 643 643 HOH HOH . F 6 HOH L 20 644 644 HOH HOH . F 6 HOH L 21 645 645 HOH HOH . F 6 HOH L 22 646 646 HOH HOH . F 6 HOH L 23 647 647 HOH HOH . F 6 HOH L 24 648 648 HOH HOH . F 6 HOH L 25 649 649 HOH HOH . F 6 HOH L 26 651 651 HOH HOH . F 6 HOH L 27 652 652 HOH HOH . F 6 HOH L 28 654 654 HOH HOH . F 6 HOH L 29 655 655 HOH HOH . F 6 HOH L 30 657 657 HOH HOH . F 6 HOH L 31 659 659 HOH HOH . F 6 HOH L 32 660 660 HOH HOH . F 6 HOH L 33 662 662 HOH HOH . F 6 HOH L 34 663 663 HOH HOH . F 6 HOH L 35 664 664 HOH HOH . F 6 HOH L 36 666 666 HOH HOH . F 6 HOH L 37 667 667 HOH HOH . F 6 HOH L 38 668 668 HOH HOH . F 6 HOH L 39 669 669 HOH HOH . F 6 HOH L 40 670 670 HOH HOH . F 6 HOH L 41 672 672 HOH HOH . F 6 HOH L 42 673 673 HOH HOH . F 6 HOH L 43 674 674 HOH HOH . F 6 HOH L 44 676 676 HOH HOH . F 6 HOH L 45 677 677 HOH HOH . F 6 HOH L 46 678 678 HOH HOH . F 6 HOH L 47 679 679 HOH HOH . F 6 HOH L 48 680 680 HOH HOH . F 6 HOH L 49 681 681 HOH HOH . F 6 HOH L 50 682 682 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 5 605 605 HOH HOH . G 6 HOH H 6 606 606 HOH HOH . G 6 HOH H 7 611 611 HOH HOH . G 6 HOH H 8 615 615 HOH HOH . G 6 HOH H 9 617 617 HOH HOH . G 6 HOH H 10 618 618 HOH HOH . G 6 HOH H 11 619 619 HOH HOH . G 6 HOH H 12 622 622 HOH HOH . G 6 HOH H 13 624 624 HOH HOH . G 6 HOH H 14 626 626 HOH HOH . G 6 HOH H 15 628 628 HOH HOH . G 6 HOH H 16 629 629 HOH HOH . G 6 HOH H 17 631 631 HOH HOH . G 6 HOH H 18 632 632 HOH HOH . G 6 HOH H 19 633 633 HOH HOH . G 6 HOH H 20 634 634 HOH HOH . G 6 HOH H 21 637 637 HOH HOH . G 6 HOH H 22 638 638 HOH HOH . G 6 HOH H 23 641 641 HOH HOH . G 6 HOH H 24 642 642 HOH HOH . G 6 HOH H 25 650 650 HOH HOH . G 6 HOH H 26 653 653 HOH HOH . G 6 HOH H 27 656 656 HOH HOH . G 6 HOH H 28 658 658 HOH HOH . G 6 HOH H 29 661 661 HOH HOH . G 6 HOH H 30 665 665 HOH HOH . G 6 HOH H 31 671 671 HOH HOH . G 6 HOH H 32 675 675 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 O OP3 DI . . . E 5 -15.361 15.452 51.245 1 42.15 ? OP3 DI 901 L 1 HETATM 2 P P DI . . . E 5 -16.409 15.975 52.146 1 42.55 ? P DI 901 L 1 HETATM 3 O OP1 DI . . . E 5 -16.679 17.417 52.004 1 45.75 ? OP1 DI 901 L 1 HETATM 4 O OP2 DI . . . E 5 -16.352 15.542 53.552 1 47.61 ? OP2 DI 901 L 1 HETATM 5 O O5' DI . . . E 5 -17.75 15.248 51.645 1 45.75 ? O5' DI 901 L 1 HETATM 6 C C5' DI . . . E 5 -19.065 15.763 51.944 1 40.95 ? C5' DI 901 L 1 HETATM 7 C C4' DI . . . E 5 -19.793 15.9 50.615 1 43.8 ? C4' DI 901 L 1 HETATM 8 O O4' DI . . . E 5 -19.631 17.094 49.85 1 44.35 ? O4' DI 901 L 1 HETATM 9 C C3' DI . . . E 5 -19.851 14.766 49.608 1 43.63 ? C3' DI 901 L 1 HETATM 10 O O3' DI . . . E 5 -21.122 14.127 49.48 1 49.73 ? O3' DI 901 L 1 HETATM 11 C C2' DI . . . E 5 -19.128 15.236 48.365 1 39.14 ? C2' DI 901 L 1 HETATM 12 C C1' DI . . . E 5 -18.906 16.685 48.701 1 38.18 ? C1' DI 901 L 1 HETATM 13 N N9 DI . . . E 5 -17.632 17.352 48.459 1 39.08 ? N9 DI 901 L 1 HETATM 14 C C8 DI . . . E 5 -16.432 16.806 48.653 1 41.01 ? C8 DI 901 L 1 HETATM 15 N N7 DI . . . E 5 -15.502 17.522 48.021 1 40.93 ? N7 DI 901 L 1 HETATM 16 C C5 DI . . . E 5 -16.126 18.535 47.434 1 36.12 ? C5 DI 901 L 1 HETATM 17 C C6 DI . . . E 5 -15.563 19.836 46.887 1 35.07 ? C6 DI 901 L 1 HETATM 18 O O6 DI . . . E 5 -14.386 20.194 46.817 1 34.48 ? O6 DI 901 L 1 HETATM 19 N N1 DI . . . E 5 -16.593 20.697 46.543 1 36.28 ? N1 DI 901 L 1 HETATM 20 C C2 DI . . . E 5 -17.942 20.466 46.69 1 32.75 ? C2 DI 901 L 1 HETATM 21 N N3 DI . . . E 5 -18.363 19.371 47.307 1 36.02 ? N3 DI 901 L 1 HETATM 22 C C4 DI . . . E 5 -17.485 18.433 47.705 1 37.04 ? C4 DI 901 L 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 397 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #