data_1MF0 # _model_server_result.job_id 11gqYFvskjxFQzGGra9uRw _model_server_result.datetime_utc '2024-11-14 16:52:41' _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 1mf0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1452}' # _entry.id 1MF0 # _exptl.entry_id 1MF0 _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 1MF0 _cell.length_a 70.6 _cell.length_b 70.6 _cell.length_c 198.39 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MF0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_775 -y+2,-x+2,-z+1/2 0 -1 0 -1 0 0 0 0 -1 141.2 141.2 99.195 # _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 metalc ? metalc1 A OD1 ASP 43 A ASP 43 1_555 B MG MG . A MG 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc2 A O GLY 70 A GLY 70 1_555 B MG MG . A MG 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc3 C O1 PO4 . A PO4 1451 1_555 B MG MG . A MG 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc4 E O2A GDP . A GDP 1452 1_555 B MG MG . A MG 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc5 E O2B GDP . A GDP 1452 1_555 B MG MG . A MG 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? # _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 122 n n PB O2B GDP sing 123 n n PB O3B GDP sing 124 n n PB O3A GDP sing 125 n n O2B HOB2 GDP sing 126 n n O3B HOB3 GDP sing 127 n n O3A PA GDP sing 128 n n PA O1A GDP doub 129 n n PA O2A GDP sing 130 n n PA O5' GDP sing 131 n n O2A HOA2 GDP sing 132 n n O5' C5' GDP sing 133 n n C5' C4' GDP sing 134 n n C5' H5' GDP sing 135 n n C5' "H5''" GDP sing 136 n n C4' O4' GDP sing 137 n n C4' C3' GDP sing 138 n n C4' H4' GDP sing 139 n n O4' C1' GDP sing 140 n n C3' O3' GDP sing 141 n n C3' C2' GDP sing 142 n n C3' H3' GDP sing 143 n n O3' HO3' GDP sing 144 n n C2' O2' GDP sing 145 n n C2' C1' GDP sing 146 n n C2' H2' GDP sing 147 n n O2' HO2' GDP sing 148 n n C1' N9 GDP sing 149 n n C1' H1' GDP sing 150 n n N9 C8 GDP sing 151 n y N9 C4 GDP sing 152 n y C8 N7 GDP doub 153 n y C8 H8 GDP sing 154 n n N7 C5 GDP sing 155 n y C5 C6 GDP sing 156 n n C5 C4 GDP doub 157 n y C6 O6 GDP doub 158 n n C6 N1 GDP sing 159 n n N1 C2 GDP sing 160 n n N1 HN1 GDP sing 161 n n C2 N2 GDP sing 162 n n C2 N3 GDP doub 163 n n N2 HN21 GDP sing 164 n n N2 HN22 GDP sing 165 n n N3 C4 GDP sing 166 n n # _atom_sites.entry_id 1MF0 _atom_sites.fract_transf_matrix[1][1] 0.014164 _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] 0.014164 _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] 0.005041 _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 B 2 MG A 1 1453 453 MG MG . C 3 PO4 A 1 1451 451 PO4 PI . D 4 AMP A 1 1454 450 AMP AMP . E 5 GDP A 1 1452 452 GDP GDP . F 6 HOH A 1 501 501 HOH TIP . F 6 HOH A 2 502 502 HOH TIP . F 6 HOH A 3 503 503 HOH TIP . F 6 HOH A 4 504 504 HOH TIP . F 6 HOH A 5 505 505 HOH TIP . F 6 HOH A 6 506 506 HOH TIP . F 6 HOH A 7 507 507 HOH TIP . F 6 HOH A 8 508 508 HOH TIP . F 6 HOH A 9 509 509 HOH TIP . F 6 HOH A 10 510 510 HOH TIP . F 6 HOH A 11 511 511 HOH TIP . F 6 HOH A 12 512 512 HOH TIP . F 6 HOH A 13 513 513 HOH TIP . F 6 HOH A 14 514 514 HOH TIP . F 6 HOH A 15 515 515 HOH TIP . F 6 HOH A 16 516 516 HOH TIP . F 6 HOH A 17 517 517 HOH TIP . F 6 HOH A 18 518 518 HOH TIP . F 6 HOH A 19 519 519 HOH TIP . F 6 HOH A 20 520 520 HOH TIP . F 6 HOH A 21 521 521 HOH TIP . F 6 HOH A 22 522 522 HOH TIP . F 6 HOH A 23 523 523 HOH TIP . F 6 HOH A 24 524 524 HOH TIP . F 6 HOH A 25 525 525 HOH TIP . F 6 HOH A 26 526 526 HOH TIP . F 6 HOH A 27 527 527 HOH TIP . F 6 HOH A 28 528 528 HOH TIP . F 6 HOH A 29 529 529 HOH TIP . F 6 HOH A 30 530 530 HOH TIP . F 6 HOH A 31 531 531 HOH TIP . F 6 HOH A 32 532 532 HOH TIP . F 6 HOH A 33 533 533 HOH TIP . F 6 HOH A 34 534 534 HOH TIP . F 6 HOH A 35 535 535 HOH TIP . F 6 HOH A 36 536 536 HOH TIP . F 6 HOH A 37 537 537 HOH TIP . F 6 HOH A 38 538 538 HOH TIP . F 6 HOH A 39 539 539 HOH TIP . F 6 HOH A 40 540 540 HOH TIP . F 6 HOH A 41 541 541 HOH TIP . F 6 HOH A 42 542 542 HOH TIP . F 6 HOH A 43 543 543 HOH TIP . F 6 HOH A 44 544 544 HOH TIP . F 6 HOH A 45 545 545 HOH TIP . F 6 HOH A 46 546 546 HOH TIP . F 6 HOH A 47 547 547 HOH TIP . F 6 HOH A 48 548 548 HOH TIP . F 6 HOH A 49 549 549 HOH TIP . F 6 HOH A 50 550 550 HOH TIP . F 6 HOH A 51 551 551 HOH TIP . F 6 HOH A 52 552 552 HOH TIP . F 6 HOH A 53 553 553 HOH TIP . F 6 HOH A 54 554 554 HOH TIP . F 6 HOH A 55 555 555 HOH TIP . F 6 HOH A 56 556 556 HOH TIP . F 6 HOH A 57 557 557 HOH TIP . F 6 HOH A 58 558 558 HOH TIP . F 6 HOH A 59 559 559 HOH TIP . F 6 HOH A 60 560 560 HOH TIP . F 6 HOH A 61 561 561 HOH TIP . F 6 HOH A 62 562 562 HOH TIP . F 6 HOH A 63 563 563 HOH TIP . F 6 HOH A 64 564 564 HOH TIP . F 6 HOH A 65 565 565 HOH TIP . F 6 HOH A 66 566 566 HOH TIP . F 6 HOH A 67 567 567 HOH TIP . F 6 HOH A 68 568 568 HOH TIP . F 6 HOH A 69 569 569 HOH TIP . F 6 HOH A 70 570 570 HOH TIP . F 6 HOH A 71 571 571 HOH TIP . F 6 HOH A 72 572 572 HOH TIP . F 6 HOH A 73 573 573 HOH TIP . F 6 HOH A 74 574 574 HOH TIP . F 6 HOH A 75 575 575 HOH TIP . F 6 HOH A 76 576 576 HOH TIP . F 6 HOH A 77 577 577 HOH TIP . F 6 HOH A 78 578 578 HOH TIP . F 6 HOH A 79 579 579 HOH TIP . F 6 HOH A 80 580 580 HOH TIP . F 6 HOH A 81 581 581 HOH TIP . F 6 HOH A 82 582 582 HOH TIP . F 6 HOH A 83 583 583 HOH TIP . F 6 HOH A 84 584 584 HOH TIP . F 6 HOH A 85 585 585 HOH TIP . F 6 HOH A 86 586 586 HOH TIP . F 6 HOH A 87 587 587 HOH TIP . F 6 HOH A 88 588 588 HOH TIP . F 6 HOH A 89 589 589 HOH TIP . F 6 HOH A 90 590 590 HOH TIP . F 6 HOH A 91 591 591 HOH TIP . F 6 HOH A 92 592 592 HOH TIP . F 6 HOH A 93 593 593 HOH TIP . F 6 HOH A 94 594 594 HOH TIP . F 6 HOH A 95 595 595 HOH TIP . F 6 HOH A 96 596 596 HOH TIP . F 6 HOH A 97 597 597 HOH TIP . F 6 HOH A 98 598 598 HOH TIP . F 6 HOH A 99 599 599 HOH TIP . F 6 HOH A 100 600 600 HOH TIP . F 6 HOH A 101 601 601 HOH TIP . F 6 HOH A 102 602 602 HOH TIP . F 6 HOH A 103 603 603 HOH TIP . F 6 HOH A 104 604 604 HOH TIP . F 6 HOH A 105 605 605 HOH TIP . F 6 HOH A 106 606 606 HOH TIP . F 6 HOH A 107 607 607 HOH TIP . # 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 64.527 53.53 36.424 1 29.02 ? PB GDP 1452 A 1 HETATM 2 O O1B GDP . . . E 5 64.302 52.535 37.551 1 23.55 ? O1B GDP 1452 A 1 HETATM 3 O O2B GDP . . . E 5 63.76 54.826 36.627 1 26.63 ? O2B GDP 1452 A 1 HETATM 4 O O3B GDP . . . E 5 65.989 53.771 36.107 1 28.2 ? O3B GDP 1452 A 1 HETATM 5 O O3A GDP . . . E 5 63.911 52.84 35.082 1 29.57 ? O3A GDP 1452 A 1 HETATM 6 P PA GDP . . . E 5 62.337 52.94 34.673 1 34.41 ? PA GDP 1452 A 1 HETATM 7 O O1A GDP . . . E 5 61.667 51.79 35.326 1 34.66 ? O1A GDP 1452 A 1 HETATM 8 O O2A GDP . . . E 5 61.968 54.323 35.08 1 31.38 ? O2A GDP 1452 A 1 HETATM 9 O O5' GDP . . . E 5 62.055 52.814 33.113 1 32.8 ? O5' GDP 1452 A 1 HETATM 10 C C5' GDP . . . E 5 62.85 51.974 32.291 1 31.76 ? C5' GDP 1452 A 1 HETATM 11 C C4' GDP . . . E 5 61.978 50.993 31.55 1 29.95 ? C4' GDP 1452 A 1 HETATM 12 O O4' GDP . . . E 5 62.786 50.181 30.67 1 28.65 ? O4' GDP 1452 A 1 HETATM 13 C C3' GDP . . . E 5 61.2 50.038 32.442 1 32.6 ? C3' GDP 1452 A 1 HETATM 14 O O3' GDP . . . E 5 59.842 49.964 32.02 1 37.08 ? O3' GDP 1452 A 1 HETATM 15 C C2' GDP . . . E 5 61.947 48.716 32.309 1 30.55 ? C2' GDP 1452 A 1 HETATM 16 O O2' GDP . . . E 5 61.091 47.601 32.456 1 30.23 ? O2' GDP 1452 A 1 HETATM 17 C C1' GDP . . . E 5 62.506 48.817 30.892 1 28.86 ? C1' GDP 1452 A 1 HETATM 18 N N9 GDP . . . E 5 63.752 48.089 30.697 1 30.68 ? N9 GDP 1452 A 1 HETATM 19 C C8 GDP . . . E 5 64.836 48.05 31.538 1 30.32 ? C8 GDP 1452 A 1 HETATM 20 N N7 GDP . . . E 5 65.828 47.345 31.06 1 33.74 ? N7 GDP 1452 A 1 HETATM 21 C C5 GDP . . . E 5 65.361 46.883 29.835 1 32.92 ? C5 GDP 1452 A 1 HETATM 22 C C6 GDP . . . E 5 65.988 46.064 28.853 1 32.55 ? C6 GDP 1452 A 1 HETATM 23 O O6 GDP . . . E 5 67.122 45.571 28.862 1 29.91 ? O6 GDP 1452 A 1 HETATM 24 N N1 GDP . . . E 5 65.145 45.835 27.769 1 35.43 ? N1 GDP 1452 A 1 HETATM 25 C C2 GDP . . . E 5 63.866 46.325 27.641 1 34.07 ? C2 GDP 1452 A 1 HETATM 26 N N2 GDP . . . E 5 63.201 45.985 26.526 1 31.4 ? N2 GDP 1452 A 1 HETATM 27 N N3 GDP . . . E 5 63.279 47.09 28.541 1 34.53 ? N3 GDP 1452 A 1 HETATM 28 C C4 GDP . . . E 5 64.077 47.326 29.605 1 32.33 ? C4 GDP 1452 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #