data_5C2J # _model_server_result.job_id 76vi5kkPuagNvgMLpbszkA _model_server_result.datetime_utc '2024-11-28 18:35:23' _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 5c2j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5C2J # _exptl.entry_id 5C2J _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 96.67 _cell.angle_gamma 90 _cell.entry_id 5C2J _cell.length_a 43.324 _cell.length_b 74.237 _cell.length_c 55.423 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C2J _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 B SG CYS 112 B CYS 105 1_555 B SG CYS 195 B CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc1 B OG1 THR 24 B THR 17 1_555 C MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.866 ? metalc ? metalc2 B OG1 THR 42 B THR 35 1_555 C MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc3 C MG MG . B MG 500 1_555 D O2B GDP . B GDP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc4 C MG MG . B MG 500 1_555 G O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc5 C MG MG . B MG 500 1_555 G O HOH . B HOH 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? # _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 5C2J _atom_sites.fract_transf_matrix[1][1] 0.023082 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002698 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01347 _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] 0.018166 _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 B 1 500 500 MG MG2 . D 4 GDP B 1 501 501 GDP GDP . E 5 AF3 B 1 502 502 AF3 AF3 . F 6 HOH A 1 601 66 HOH TIP . F 6 HOH A 2 602 2 HOH TIP . F 6 HOH A 3 603 57 HOH TIP . F 6 HOH A 4 604 59 HOH TIP . F 6 HOH A 5 605 65 HOH TIP . F 6 HOH A 6 606 36 HOH TIP . F 6 HOH A 7 607 68 HOH TIP . F 6 HOH A 8 608 7 HOH TIP . F 6 HOH A 9 609 20 HOH TIP . F 6 HOH A 10 610 97 HOH TIP . F 6 HOH A 11 611 54 HOH TIP . F 6 HOH A 12 612 85 HOH TIP . F 6 HOH A 13 613 48 HOH TIP . F 6 HOH A 14 614 14 HOH TIP . F 6 HOH A 15 615 60 HOH TIP . F 6 HOH A 16 616 91 HOH TIP . F 6 HOH A 17 617 99 HOH TIP . F 6 HOH A 18 618 49 HOH TIP . F 6 HOH A 19 619 93 HOH TIP . F 6 HOH A 20 620 27 HOH TIP . F 6 HOH A 21 621 40 HOH TIP . F 6 HOH A 22 622 42 HOH TIP . F 6 HOH A 23 623 30 HOH TIP . F 6 HOH A 24 624 24 HOH TIP . F 6 HOH A 25 625 56 HOH TIP . F 6 HOH A 26 626 3 HOH TIP . F 6 HOH A 27 627 16 HOH TIP . F 6 HOH A 28 628 39 HOH TIP . F 6 HOH A 29 629 1 HOH TIP . F 6 HOH A 30 630 86 HOH TIP . F 6 HOH A 31 631 84 HOH TIP . F 6 HOH A 32 632 50 HOH TIP . F 6 HOH A 33 633 87 HOH TIP . F 6 HOH A 34 634 90 HOH TIP . F 6 HOH A 35 635 100 HOH TIP . F 6 HOH A 36 636 4 HOH TIP . F 6 HOH A 37 637 41 HOH TIP . F 6 HOH A 38 638 44 HOH TIP . F 6 HOH A 39 639 10 HOH TIP . F 6 HOH A 40 640 77 HOH TIP . F 6 HOH A 41 641 53 HOH TIP . F 6 HOH A 42 642 62 HOH TIP . F 6 HOH A 43 643 15 HOH TIP . F 6 HOH A 44 644 82 HOH TIP . F 6 HOH A 45 645 34 HOH TIP . F 6 HOH A 46 646 69 HOH TIP . G 6 HOH B 1 601 73 HOH TIP . G 6 HOH B 2 602 94 HOH TIP . G 6 HOH B 3 603 31 HOH TIP . G 6 HOH B 4 604 101 HOH TIP . G 6 HOH B 5 605 33 HOH TIP . G 6 HOH B 6 606 37 HOH TIP . G 6 HOH B 7 607 11 HOH TIP . G 6 HOH B 8 608 28 HOH TIP . G 6 HOH B 9 609 6 HOH TIP . G 6 HOH B 10 610 75 HOH TIP . G 6 HOH B 11 611 23 HOH TIP . G 6 HOH B 12 612 46 HOH TIP . G 6 HOH B 13 613 96 HOH TIP . G 6 HOH B 14 614 13 HOH TIP . G 6 HOH B 15 615 25 HOH TIP . G 6 HOH B 16 616 12 HOH TIP . G 6 HOH B 17 617 9 HOH TIP . G 6 HOH B 18 618 95 HOH TIP . G 6 HOH B 19 619 89 HOH TIP . G 6 HOH B 20 620 29 HOH TIP . G 6 HOH B 21 621 76 HOH TIP . G 6 HOH B 22 622 26 HOH TIP . G 6 HOH B 23 623 79 HOH TIP . G 6 HOH B 24 624 38 HOH TIP . G 6 HOH B 25 625 58 HOH TIP . G 6 HOH B 26 626 72 HOH TIP . G 6 HOH B 27 627 55 HOH TIP . G 6 HOH B 28 628 17 HOH TIP . G 6 HOH B 29 629 74 HOH TIP . G 6 HOH B 30 630 81 HOH TIP . G 6 HOH B 31 631 8 HOH TIP . G 6 HOH B 32 632 103 HOH TIP . G 6 HOH B 33 633 35 HOH TIP . G 6 HOH B 34 634 5 HOH TIP . G 6 HOH B 35 635 22 HOH TIP . G 6 HOH B 36 636 52 HOH TIP . G 6 HOH B 37 637 88 HOH TIP . G 6 HOH B 38 638 98 HOH TIP . G 6 HOH B 39 639 67 HOH TIP . G 6 HOH B 40 640 64 HOH TIP . G 6 HOH B 41 641 70 HOH TIP . G 6 HOH B 42 642 71 HOH TIP . G 6 HOH B 43 643 78 HOH TIP . G 6 HOH B 44 644 19 HOH TIP . G 6 HOH B 45 645 83 HOH TIP . G 6 HOH B 46 646 43 HOH TIP . G 6 HOH B 47 647 32 HOH TIP . G 6 HOH B 48 648 51 HOH TIP . G 6 HOH B 49 649 63 HOH TIP . G 6 HOH B 50 650 21 HOH TIP . G 6 HOH B 51 651 102 HOH TIP . G 6 HOH B 52 652 47 HOH TIP . G 6 HOH B 53 653 18 HOH TIP . G 6 HOH B 54 654 45 HOH TIP . G 6 HOH B 55 655 92 HOH TIP . G 6 HOH B 56 656 61 HOH TIP . G 6 HOH B 57 657 80 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 . . . D 4 -3.641 1.636 -0.326 1 19.84 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . D 4 -5.096 1.514 -0.568 1 21.64 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . D 4 -3.079 3.125 -0.564 1 16.04 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . D 4 -3.246 1.242 1.182 1 17.16 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . D 4 -2.796 0.669 -1.299 1 22.58 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . D 4 -1.349 1.086 -1.871 1 22.76 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . D 4 -1.553 1.805 -3.148 1 22.16 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . D 4 -0.595 1.762 -0.792 1 21.05 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . D 4 -0.682 -0.341 -2.212 1 24.96 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . D 4 -0.582 -1.357 -1.21 1 26.91 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . D 4 0.204 -2.572 -1.71 1 26.58 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . D 4 -0.443 -3.096 -2.884 1 25.26 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . D 4 1.598 -2.128 -2.162 1 27.25 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . D 4 2.481 -3.252 -2.173 1 28.9 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . D 4 1.293 -1.714 -3.599 1 28.07 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . D 4 2.508 -1.695 -4.355 1 27.13 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . D 4 0.472 -2.944 -3.984 1 26.73 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . D 4 -0.254 -2.722 -5.255 1 27.21 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . D 4 -1.081 -1.709 -5.504 1 27.01 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . D 4 -1.582 -1.834 -6.73 1 26.25 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . D 4 -1.072 -2.937 -7.269 1 27.68 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . D 4 -1.254 -3.558 -8.499 1 28.27 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . D 4 -1.988 -3.061 -9.351 1 28.45 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . D 4 -0.571 -4.753 -8.756 1 28.88 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . D 4 0.277 -5.277 -7.773 1 28.19 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . D 4 0.943 -6.402 -8.015 1 25.87 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . D 4 0.428 -4.649 -6.597 1 27.74 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . D 4 -0.222 -3.507 -6.329 1 27.67 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 510 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #