data_1GRN # _model_server_result.job_id ivrvkY8HrW9pQHxSbgEYpA _model_server_result.datetime_utc '2024-11-22 13:15:48' _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 1grn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":198}' # _entry.id 1GRN # _exptl.entry_id 1GRN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 1GRN _cell.length_a 52.4 _cell.length_b 69 _cell.length_c 129.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GRN _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 4 _struct_asym.id D _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 105 A CYS 105 1_555 A SG CYS 188 A CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A OG1 THR 17 A THR 17 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc2 A OG1 THR 35 A THR 35 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc3 D O2B GDP . A GDP 198 1_555 C MG MG . A MG 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc4 D O3B GDP . A GDP 198 1_555 E AL AF3 . A AF3 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc5 D O2B GDP . A GDP 198 1_555 E AL AF3 . A AF3 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.614 ? metalc ? metalc6 C MG MG . A MG 199 1_555 E F3 AF3 . A AF3 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc7 C MG MG . A MG 199 1_555 E AL AF3 . A AF3 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.622 ? metalc ? metalc8 C MG MG . A MG 199 1_555 F O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc9 C MG MG . A MG 199 1_555 F O HOH . A HOH 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc10 E AL AF3 . A AF3 200 1_555 F O HOH . A HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? # _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 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 1GRN _atom_sites.fract_transf_matrix[1][1] 0.019084 _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] 0.014493 _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] 0.007716 _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 MG A 1 199 199 MG MG . D 4 GDP A 1 198 198 GDP GDP . E 5 AF3 A 1 200 200 AF3 FLA . F 6 HOH A 1 503 503 HOH HOH . F 6 HOH A 2 504 504 HOH HOH . F 6 HOH A 3 505 505 HOH HOH . F 6 HOH A 4 507 507 HOH HOH . F 6 HOH A 5 508 508 HOH HOH . F 6 HOH A 6 509 509 HOH HOH . F 6 HOH A 7 511 511 HOH HOH . F 6 HOH A 8 512 512 HOH HOH . F 6 HOH A 9 513 513 HOH HOH . F 6 HOH A 10 514 514 HOH HOH . F 6 HOH A 11 516 516 HOH HOH . F 6 HOH A 12 517 517 HOH HOH . F 6 HOH A 13 518 518 HOH HOH . F 6 HOH A 14 521 521 HOH HOH . F 6 HOH A 15 522 522 HOH HOH . F 6 HOH A 16 526 526 HOH HOH . F 6 HOH A 17 527 527 HOH HOH . F 6 HOH A 18 528 528 HOH HOH . F 6 HOH A 19 529 529 HOH HOH . F 6 HOH A 20 534 534 HOH HOH . F 6 HOH A 21 535 535 HOH HOH . F 6 HOH A 22 536 536 HOH HOH . F 6 HOH A 23 537 537 HOH HOH . F 6 HOH A 24 538 538 HOH HOH . F 6 HOH A 25 541 541 HOH HOH . F 6 HOH A 26 542 542 HOH HOH . F 6 HOH A 27 544 544 HOH HOH . F 6 HOH A 28 545 545 HOH HOH . F 6 HOH A 29 549 549 HOH HOH . F 6 HOH A 30 553 553 HOH HOH . F 6 HOH A 31 554 554 HOH HOH . F 6 HOH A 32 555 555 HOH HOH . F 6 HOH A 33 556 556 HOH HOH . F 6 HOH A 34 557 557 HOH HOH . F 6 HOH A 35 558 558 HOH HOH . F 6 HOH A 36 561 561 HOH HOH . F 6 HOH A 37 566 566 HOH HOH . F 6 HOH A 38 570 570 HOH HOH . F 6 HOH A 39 571 571 HOH HOH . G 6 HOH B 1 501 501 HOH HOH . G 6 HOH B 2 502 502 HOH HOH . G 6 HOH B 3 506 506 HOH HOH . G 6 HOH B 4 510 510 HOH HOH . G 6 HOH B 5 515 515 HOH HOH . G 6 HOH B 6 519 519 HOH HOH . G 6 HOH B 7 520 520 HOH HOH . G 6 HOH B 8 523 523 HOH HOH . G 6 HOH B 9 524 524 HOH HOH . G 6 HOH B 10 525 525 HOH HOH . G 6 HOH B 11 530 530 HOH HOH . G 6 HOH B 12 531 531 HOH HOH . G 6 HOH B 13 532 532 HOH HOH . G 6 HOH B 14 533 533 HOH HOH . G 6 HOH B 15 539 539 HOH HOH . G 6 HOH B 16 540 540 HOH HOH . G 6 HOH B 17 543 543 HOH HOH . G 6 HOH B 18 546 546 HOH HOH . G 6 HOH B 19 547 547 HOH HOH . G 6 HOH B 20 548 548 HOH HOH . G 6 HOH B 21 550 550 HOH HOH . G 6 HOH B 22 551 551 HOH HOH . G 6 HOH B 23 552 552 HOH HOH . G 6 HOH B 24 559 559 HOH HOH . G 6 HOH B 25 560 560 HOH HOH . G 6 HOH B 26 562 562 HOH HOH . G 6 HOH B 27 563 563 HOH HOH . G 6 HOH B 28 564 564 HOH HOH . G 6 HOH B 29 565 565 HOH HOH . G 6 HOH B 30 567 567 HOH HOH . G 6 HOH B 31 568 568 HOH HOH . G 6 HOH B 32 569 569 HOH HOH . G 6 HOH B 33 572 572 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 . . . D 4 23.873 1.221 12.151 1 21.29 ? PB GDP 198 A 1 HETATM 2 O O1B GDP . . . D 4 23.136 0.88 10.933 1 20.25 ? O1B GDP 198 A 1 HETATM 3 O O2B GDP . . . D 4 23.985 2.624 12.556 1 15.5 ? O2B GDP 198 A 1 HETATM 4 O O3B GDP . . . D 4 23.285 0.381 13.306 1 20.27 ? O3B GDP 198 A 1 HETATM 5 O O3A GDP . . . D 4 25.377 0.652 12.025 1 23.72 ? O3A GDP 198 A 1 HETATM 6 P PA GDP . . . D 4 26.773 1.425 12.276 1 22.54 ? PA GDP 198 A 1 HETATM 7 O O1A GDP . . . D 4 26.991 2.405 11.185 1 20.45 ? O1A GDP 198 A 1 HETATM 8 O O2A GDP . . . D 4 26.834 1.855 13.664 1 17.19 ? O2A GDP 198 A 1 HETATM 9 O O5' GDP . . . D 4 27.765 0.159 12.021 1 23.68 ? O5' GDP 198 A 1 HETATM 10 C C5' GDP . . . D 4 27.697 -0.992 12.871 1 19.62 ? C5' GDP 198 A 1 HETATM 11 C C4' GDP . . . D 4 29.002 -1.806 12.82 1 24.63 ? C4' GDP 198 A 1 HETATM 12 O O4' GDP . . . D 4 29.345 -2.099 11.457 1 25.12 ? O4' GDP 198 A 1 HETATM 13 C C3' GDP . . . D 4 30.224 -1.106 13.421 1 23.84 ? C3' GDP 198 A 1 HETATM 14 O O3' GDP . . . D 4 30.924 -2.011 14.244 1 29.16 ? O3' GDP 198 A 1 HETATM 15 C C2' GDP . . . D 4 31.057 -0.646 12.237 1 26.94 ? C2' GDP 198 A 1 HETATM 16 O O2' GDP . . . D 4 32.477 -0.533 12.469 1 28.07 ? O2' GDP 198 A 1 HETATM 17 C C1' GDP . . . D 4 30.688 -1.662 11.175 1 24.66 ? C1' GDP 198 A 1 HETATM 18 N N9 GDP . . . D 4 30.724 -1.085 9.826 1 23.75 ? N9 GDP 198 A 1 HETATM 19 C C8 GDP . . . D 4 29.952 -0.11 9.263 1 22.74 ? C8 GDP 198 A 1 HETATM 20 N N7 GDP . . . D 4 30.227 0.189 8.035 1 21.25 ? N7 GDP 198 A 1 HETATM 21 C C5 GDP . . . D 4 31.29 -0.668 7.736 1 23.68 ? C5 GDP 198 A 1 HETATM 22 C C6 GDP . . . D 4 32.049 -0.819 6.508 1 25.1 ? C6 GDP 198 A 1 HETATM 23 O O6 GDP . . . D 4 31.919 -0.217 5.439 1 25.93 ? O6 GDP 198 A 1 HETATM 24 N N1 GDP . . . D 4 33.04 -1.804 6.633 1 27.9 ? N1 GDP 198 A 1 HETATM 25 C C2 GDP . . . D 4 33.289 -2.551 7.776 1 25.96 ? C2 GDP 198 A 1 HETATM 26 N N2 GDP . . . D 4 34.277 -3.438 7.695 1 24.03 ? N2 GDP 198 A 1 HETATM 27 N N3 GDP . . . D 4 32.587 -2.414 8.928 1 25.14 ? N3 GDP 198 A 1 HETATM 28 C C4 GDP . . . D 4 31.607 -1.458 8.833 1 23.96 ? C4 GDP 198 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #