data_7S0Y # _model_server_result.job_id zB2z1GZRlrWHS7oHrh38hQ _model_server_result.datetime_utc '2024-11-08 06:08:15' _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 7s0y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":201}' # _entry.id 7S0Y # _exptl.entry_id 7S0Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 7S0Y _cell.length_a 122.354 _cell.length_b 140.948 _cell.length_c 111.803 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7S0Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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,H,I,J,K,L,M,N,O,P,Q,R,S _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 6 _struct_asym.id N _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 OD2 ASP 290 A ASP 288 1_555 C MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc2 A OE1 GLU 517 A GLU 515 1_555 C MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc3 C MN MN . A MN 601 1_555 D O1A UDP . A UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc4 C MN MN . A MN 601 1_555 D O1B UDP . A UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc5 C MN MN . A MN 601 1_555 R O HOH . A HOH 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc6 C MN MN . A MN 601 1_555 R O HOH . A HOH 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc7 B OG1 THR 18 B THR 17 1_555 O MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc8 N O2B GDP . B GDP 201 1_555 O MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc9 O MG MG . B MG 202 1_555 S O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc10 O MG MG . B MG 202 1_555 S O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc11 O MG MG . B MG 202 1_555 S O HOH . B HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.77 ? metalc ? metalc12 O MG MG . B MG 202 1_555 S O HOH . B HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 7S0Y _atom_sites.fract_transf_matrix[1][1] 0.008173 _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] 0.007095 _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] 0.008944 _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 MN A 1 601 1542 MN MN . D 4 UDP A 1 602 1543 UDP UDP . E 5 SO4 A 1 603 1 SO4 SO4 . F 5 SO4 A 1 604 2 SO4 SO4 . G 5 SO4 A 1 605 3 SO4 SO4 . H 5 SO4 A 1 606 4 SO4 SO4 . I 5 SO4 A 1 607 5 SO4 SO4 . J 5 SO4 A 1 608 8 SO4 SO4 . K 5 SO4 A 1 609 22 SO4 SO4 . L 5 SO4 A 1 610 23 SO4 SO4 . M 5 SO4 A 1 611 24 SO4 SO4 . N 6 GDP B 1 201 200 GDP GDP . O 7 MG B 1 202 201 MG MG . P 5 SO4 B 1 203 6 SO4 SO4 . Q 5 SO4 B 1 204 7 SO4 SO4 . R 8 HOH A 1 701 23 HOH HOH . R 8 HOH A 2 702 21 HOH HOH . R 8 HOH A 3 703 35 HOH HOH . R 8 HOH A 4 704 7 HOH HOH . R 8 HOH A 5 705 1 HOH HOH . R 8 HOH A 6 706 2 HOH HOH . R 8 HOH A 7 707 9 HOH HOH . R 8 HOH A 8 708 11 HOH HOH . R 8 HOH A 9 709 22 HOH HOH . R 8 HOH A 10 710 39 HOH HOH . R 8 HOH A 11 711 38 HOH HOH . R 8 HOH A 12 712 18 HOH HOH . R 8 HOH A 13 713 28 HOH HOH . R 8 HOH A 14 714 14 HOH HOH . R 8 HOH A 15 715 27 HOH HOH . R 8 HOH A 16 716 24 HOH HOH . S 8 HOH B 1 301 15 HOH HOH . S 8 HOH B 2 302 32 HOH HOH . S 8 HOH B 3 303 17 HOH HOH . S 8 HOH B 4 304 4 HOH HOH . S 8 HOH B 5 305 16 HOH HOH . S 8 HOH B 6 306 37 HOH HOH . S 8 HOH B 7 307 5 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 . . . N 6 -22.52 -16.868 9.638 1 66.97 ? PB GDP 201 B 1 HETATM 2 O O1B GDP . . . N 6 -23.927 -16.686 9.126 1 53.43 ? O1B GDP 201 B 1 HETATM 3 O O2B GDP . . . N 6 -21.895 -18.227 9.363 1 61.81 ? O2B GDP 201 B 1 HETATM 4 O O3B GDP . . . N 6 -22.404 -16.343 11.051 1 65.81 ? O3B GDP 201 B 1 HETATM 5 O O3A GDP . . . N 6 -21.548 -15.854 8.827 1 65.52 ? O3A GDP 201 B 1 HETATM 6 P PA GDP . . . N 6 -21.204 -15.977 7.249 1 69.96 ? PA GDP 201 B 1 HETATM 7 O O1A GDP . . . N 6 -22.049 -17.027 6.578 1 70.79 ? O1A GDP 201 B 1 HETATM 8 O O2A GDP . . . N 6 -19.703 -15.978 7.041 1 65.86 ? O2A GDP 201 B 1 HETATM 9 O O5' GDP . . . N 6 -21.844 -14.616 6.72 1 71 ? O5' GDP 201 B 1 HETATM 10 C C5' GDP . . . N 6 -21.402 -13.343 7.183 1 76.18 ? C5' GDP 201 B 1 HETATM 11 C C4' GDP . . . N 6 -21.564 -12.307 6.074 1 71.09 ? C4' GDP 201 B 1 HETATM 12 O O4' GDP . . . N 6 -20.523 -11.344 6.214 1 70.01 ? O4' GDP 201 B 1 HETATM 13 C C3' GDP . . . N 6 -21.395 -12.897 4.687 1 72.81 ? C3' GDP 201 B 1 HETATM 14 O O3' GDP . . . N 6 -22.166 -12.14 3.759 1 74.99 ? O3' GDP 201 B 1 HETATM 15 C C2' GDP . . . N 6 -19.911 -12.766 4.42 1 73.31 ? C2' GDP 201 B 1 HETATM 16 O O2' GDP . . . N 6 -19.608 -12.574 3.038 1 73.67 ? O2' GDP 201 B 1 HETATM 17 C C1' GDP . . . N 6 -19.491 -11.573 5.261 1 70.89 ? C1' GDP 201 B 1 HETATM 18 N N9 GDP . . . N 6 -18.216 -11.794 5.977 1 70.77 ? N9 GDP 201 B 1 HETATM 19 C C8 GDP . . . N 6 -17.761 -12.891 6.612 1 75.03 ? C8 GDP 201 B 1 HETATM 20 N N7 GDP . . . N 6 -16.526 -12.681 7.155 1 73.59 ? N7 GDP 201 B 1 HETATM 21 C C5 GDP . . . N 6 -16.189 -11.42 6.85 1 71.09 ? C5 GDP 201 B 1 HETATM 22 C C6 GDP . . . N 6 -15.046 -10.527 7.104 1 69.82 ? C6 GDP 201 B 1 HETATM 23 O O6 GDP . . . N 6 -14.043 -10.908 7.757 1 67.98 ? O6 GDP 201 B 1 HETATM 24 N N1 GDP . . . N 6 -15.14 -9.279 6.612 1 77.66 ? N1 GDP 201 B 1 HETATM 25 C C2 GDP . . . N 6 -16.213 -8.821 5.914 1 74.72 ? C2 GDP 201 B 1 HETATM 26 N N2 GDP . . . N 6 -16.254 -7.557 5.435 1 73.92 ? N2 GDP 201 B 1 HETATM 27 N N3 GDP . . . N 6 -17.282 -9.584 5.654 1 73.04 ? N3 GDP 201 B 1 HETATM 28 C C4 GDP . . . N 6 -17.313 -10.853 6.089 1 72 ? C4 GDP 201 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #