data_2O52 # _model_server_result.job_id LA-Du6R_UNcqwKWA6wM1Ag _model_server_result.datetime_utc '2025-02-05 12:58:36' _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 2o52 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 2O52 # _exptl.entry_id 2O52 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 2O52 _cell.length_a 67.528 _cell.length_b 67.528 _cell.length_c 179.955 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2O52 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,J 1 1 B,G,H,I,K 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 H N 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 OG SER 39 A SER 22 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc2 D O2B GDP . A GDP 601 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc3 C MG MG . A MG 602 1_555 J O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc4 C MG MG . A MG 602 1_555 J O HOH . A HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc5 C MG MG . A MG 602 1_555 J O HOH . A HOH 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc6 C MG MG . A MG 602 1_555 J O HOH . A HOH 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc7 B OG SER 39 B SER 22 1_555 G MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc8 H O2B GDP . B GDP 601 1_555 G MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc9 G MG MG . B MG 602 1_555 K O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc10 G MG MG . B MG 602 1_555 K O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc11 G MG MG . B MG 602 1_555 K O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc12 G MG MG . B MG 602 1_555 K O HOH . B HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? # _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 92 n n PB O2B GDP sing 93 n n PB O3B GDP sing 94 n n PB O3A GDP sing 95 n n O2B HOB2 GDP sing 96 n n O3B HOB3 GDP sing 97 n n O3A PA GDP sing 98 n n PA O1A GDP doub 99 n n PA O2A GDP sing 100 n n PA O5' GDP sing 101 n n O2A HOA2 GDP sing 102 n n O5' C5' GDP sing 103 n n C5' C4' GDP sing 104 n n C5' H5' GDP sing 105 n n C5' "H5''" GDP sing 106 n n C4' O4' GDP sing 107 n n C4' C3' GDP sing 108 n n C4' H4' GDP sing 109 n n O4' C1' GDP sing 110 n n C3' O3' GDP sing 111 n n C3' C2' GDP sing 112 n n C3' H3' GDP sing 113 n n O3' HO3' GDP sing 114 n n C2' O2' GDP sing 115 n n C2' C1' GDP sing 116 n n C2' H2' GDP sing 117 n n O2' HO2' GDP sing 118 n n C1' N9 GDP sing 119 n n C1' H1' GDP sing 120 n n N9 C8 GDP sing 121 n y N9 C4 GDP sing 122 n y C8 N7 GDP doub 123 n y C8 H8 GDP sing 124 n n N7 C5 GDP sing 125 n y C5 C6 GDP sing 126 n n C5 C4 GDP doub 127 n y C6 O6 GDP doub 128 n n C6 N1 GDP sing 129 n n N1 C2 GDP sing 130 n n N1 HN1 GDP sing 131 n n C2 N2 GDP sing 132 n n C2 N3 GDP doub 133 n n N2 HN21 GDP sing 134 n n N2 HN22 GDP sing 135 n n N3 C4 GDP sing 136 n n # _atom_sites.entry_id 2O52 _atom_sites.fract_transf_matrix[1][1] 0.01481 _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] 0.01481 _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] 0.00556 _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 2 MG A 1 602 602 MG MG . D 3 GDP A 1 601 601 GDP GDP . E 4 BME A 1 603 603 BME BME . F 5 UNX A 1 1003 1003 UNX UNX . G 2 MG B 1 602 602 MG MG . H 3 GDP B 1 601 601 GDP GDP . I 4 BME B 1 603 603 BME BME . J 6 HOH A 1 1004 7 HOH HOH . J 6 HOH A 2 1005 8 HOH HOH . J 6 HOH A 3 1006 9 HOH HOH . J 6 HOH A 4 1007 10 HOH HOH . J 6 HOH A 5 1008 11 HOH HOH . J 6 HOH A 6 1009 12 HOH HOH . J 6 HOH A 7 1010 13 HOH HOH . J 6 HOH A 8 1011 14 HOH HOH . J 6 HOH A 9 1012 15 HOH HOH . J 6 HOH A 10 1013 16 HOH HOH . J 6 HOH A 11 1014 17 HOH HOH . J 6 HOH A 12 1015 18 HOH HOH . J 6 HOH A 13 1016 20 HOH HOH . J 6 HOH A 14 1017 21 HOH HOH . J 6 HOH A 15 1018 22 HOH HOH . J 6 HOH A 16 1019 23 HOH HOH . J 6 HOH A 17 1020 24 HOH HOH . J 6 HOH A 18 1021 25 HOH HOH . J 6 HOH A 19 1022 26 HOH HOH . J 6 HOH A 20 1023 27 HOH HOH . J 6 HOH A 21 1024 28 HOH HOH . J 6 HOH A 22 1025 29 HOH HOH . J 6 HOH A 23 1026 30 HOH HOH . J 6 HOH A 24 1027 31 HOH HOH . J 6 HOH A 25 1028 32 HOH HOH . J 6 HOH A 26 1029 33 HOH HOH . J 6 HOH A 27 1030 34 HOH HOH . J 6 HOH A 28 1031 35 HOH HOH . J 6 HOH A 29 1032 36 HOH HOH . J 6 HOH A 30 1033 54 HOH HOH . J 6 HOH A 31 1034 55 HOH HOH . J 6 HOH A 32 1035 56 HOH HOH . J 6 HOH A 33 1036 63 HOH HOH . J 6 HOH A 34 1037 64 HOH HOH . J 6 HOH A 35 1038 67 HOH HOH . J 6 HOH A 36 1039 69 HOH HOH . J 6 HOH A 37 1040 72 HOH HOH . J 6 HOH A 38 1041 73 HOH HOH . K 6 HOH B 1 604 1 HOH HOH . K 6 HOH B 2 605 2 HOH HOH . K 6 HOH B 3 606 3 HOH HOH . K 6 HOH B 4 607 4 HOH HOH . K 6 HOH B 5 608 5 HOH HOH . K 6 HOH B 6 609 6 HOH HOH . K 6 HOH B 7 610 19 HOH HOH . K 6 HOH B 8 611 37 HOH HOH . K 6 HOH B 9 612 38 HOH HOH . K 6 HOH B 10 613 39 HOH HOH . K 6 HOH B 11 614 40 HOH HOH . K 6 HOH B 12 615 41 HOH HOH . K 6 HOH B 13 616 42 HOH HOH . K 6 HOH B 14 617 43 HOH HOH . K 6 HOH B 15 618 44 HOH HOH . K 6 HOH B 16 619 45 HOH HOH . K 6 HOH B 17 620 46 HOH HOH . K 6 HOH B 18 621 47 HOH HOH . K 6 HOH B 19 622 48 HOH HOH . K 6 HOH B 20 623 49 HOH HOH . K 6 HOH B 21 624 50 HOH HOH . K 6 HOH B 22 625 51 HOH HOH . K 6 HOH B 23 626 52 HOH HOH . K 6 HOH B 24 627 53 HOH HOH . K 6 HOH B 25 628 57 HOH HOH . K 6 HOH B 26 629 58 HOH HOH . K 6 HOH B 27 630 59 HOH HOH . K 6 HOH B 28 631 60 HOH HOH . K 6 HOH B 29 632 61 HOH HOH . K 6 HOH B 30 633 62 HOH HOH . K 6 HOH B 31 634 65 HOH HOH . K 6 HOH B 32 635 66 HOH HOH . K 6 HOH B 33 636 68 HOH HOH . K 6 HOH B 34 637 70 HOH HOH . K 6 HOH B 35 638 71 HOH HOH . K 6 HOH B 36 639 74 HOH HOH . K 6 HOH B 37 640 75 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 3 21.032 -12.625 1.751 1 33.89 ? PB GDP 601 A 1 HETATM 2 O O1B GDP . . . D 3 21.088 -14.034 1.248 1 30.96 ? O1B GDP 601 A 1 HETATM 3 O O2B GDP . . . D 3 19.746 -12.367 2.46 1 34 ? O2B GDP 601 A 1 HETATM 4 O O3B GDP . . . D 3 22.174 -12.374 2.69 1 38.24 ? O3B GDP 601 A 1 HETATM 5 O O3A GDP . . . D 3 21.169 -11.625 0.499 1 36.16 ? O3A GDP 601 A 1 HETATM 6 P PA GDP . . . D 3 20.603 -10.119 0.436 1 33.02 ? PA GDP 601 A 1 HETATM 7 O O1A GDP . . . D 3 19.129 -10.078 0.124 1 33.08 ? O1A GDP 601 A 1 HETATM 8 O O2A GDP . . . D 3 20.94 -9.342 1.672 1 33.93 ? O2A GDP 601 A 1 HETATM 9 O O5' GDP . . . D 3 21.44 -9.6 -0.851 1 37.9 ? O5' GDP 601 A 1 HETATM 10 C C5' GDP . . . D 3 22.839 -9.348 -0.702 1 39.35 ? C5' GDP 601 A 1 HETATM 11 C C4' GDP . . . D 3 23.341 -8.452 -1.827 1 38.75 ? C4' GDP 601 A 1 HETATM 12 O O4' GDP . . . D 3 23.011 -9.002 -3.108 1 35.09 ? O4' GDP 601 A 1 HETATM 13 C C3' GDP . . . D 3 22.694 -7.088 -1.756 1 39.16 ? C3' GDP 601 A 1 HETATM 14 O O3' GDP . . . D 3 23.691 -6.122 -2.042 1 44.17 ? O3' GDP 601 A 1 HETATM 15 C C2' GDP . . . D 3 21.582 -7.157 -2.785 1 40.53 ? C2' GDP 601 A 1 HETATM 16 O O2' GDP . . . D 3 21.17 -5.898 -3.34 1 43.56 ? O2' GDP 601 A 1 HETATM 17 C C1' GDP . . . D 3 22.171 -8.086 -3.811 1 38.3 ? C1' GDP 601 A 1 HETATM 18 N N9 GDP . . . D 3 21.151 -8.841 -4.565 1 38.17 ? N9 GDP 601 A 1 HETATM 19 C C8 GDP . . . D 3 20.178 -9.61 -4.105 1 37.81 ? C8 GDP 601 A 1 HETATM 20 N N7 GDP . . . D 3 19.476 -10.15 -5.127 1 38.5 ? N7 GDP 601 A 1 HETATM 21 C C5 GDP . . . D 3 20.002 -9.727 -6.267 1 39.51 ? C5 GDP 601 A 1 HETATM 22 C C6 GDP . . . D 3 19.763 -9.895 -7.716 1 38.73 ? C6 GDP 601 A 1 HETATM 23 O O6 GDP . . . D 3 18.831 -10.615 -8.15 1 38.76 ? O6 GDP 601 A 1 HETATM 24 N N1 GDP . . . D 3 20.594 -9.254 -8.565 1 38.64 ? N1 GDP 601 A 1 HETATM 25 C C2 GDP . . . D 3 21.608 -8.474 -8.142 1 38.89 ? C2 GDP 601 A 1 HETATM 26 N N2 GDP . . . D 3 22.428 -7.842 -9.034 1 40.07 ? N2 GDP 601 A 1 HETATM 27 N N3 GDP . . . D 3 21.863 -8.281 -6.843 1 38.8 ? N3 GDP 601 A 1 HETATM 28 C C4 GDP . . . D 3 21.118 -8.873 -5.885 1 41.11 ? C4 GDP 601 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #