data_3VOB # _model_server_result.job_id F30Kp6MDP8zdTwJ_yPfI6Q _model_server_result.datetime_utc '2024-11-05 04:42:36' _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 3vob # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 3VOB # _exptl.entry_id 3VOB _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.95 _cell.angle_gamma 90 _cell.entry_id 3VOB _cell.length_a 72.095 _cell.length_b 50.507 _cell.length_c 88.288 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VOB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _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 O LEU 192 A LEU 200 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc2 A O VAL 195 A VAL 203 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc3 A OD1 ASN 200 A ASN 208 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc4 A O LEU 201 A LEU 209 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc5 B CA CA . A CA 401 1_555 D O 9PC . A 9PC 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.116 ? metalc ? metalc6 B CA CA . A CA 401 1_555 E O HOH . A HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.121 ? # _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 103 n n PB O2B GDP sing 104 n n PB O3B GDP sing 105 n n PB O3A GDP sing 106 n n O2B HOB2 GDP sing 107 n n O3B HOB3 GDP sing 108 n n O3A PA GDP sing 109 n n PA O1A GDP doub 110 n n PA O2A GDP sing 111 n n PA O5' GDP sing 112 n n O2A HOA2 GDP sing 113 n n O5' C5' GDP sing 114 n n C5' C4' GDP sing 115 n n C5' H5' GDP sing 116 n n C5' "H5''" GDP sing 117 n n C4' O4' GDP sing 118 n n C4' C3' GDP sing 119 n n C4' H4' GDP sing 120 n n O4' C1' GDP sing 121 n n C3' O3' GDP sing 122 n n C3' C2' GDP sing 123 n n C3' H3' GDP sing 124 n n O3' HO3' GDP sing 125 n n C2' O2' GDP sing 126 n n C2' C1' GDP sing 127 n n C2' H2' GDP sing 128 n n O2' HO2' GDP sing 129 n n C1' N9 GDP sing 130 n n C1' H1' GDP sing 131 n n N9 C8 GDP sing 132 n y N9 C4 GDP sing 133 n y C8 N7 GDP doub 134 n y C8 H8 GDP sing 135 n n N7 C5 GDP sing 136 n y C5 C6 GDP sing 137 n n C5 C4 GDP doub 138 n y C6 O6 GDP doub 139 n n C6 N1 GDP sing 140 n n N1 C2 GDP sing 141 n n N1 HN1 GDP sing 142 n n C2 N2 GDP sing 143 n n C2 N3 GDP doub 144 n n N2 HN21 GDP sing 145 n n N2 HN22 GDP sing 146 n n N3 C4 GDP sing 147 n n # _atom_sites.entry_id 3VOB _atom_sites.fract_transf_matrix[1][1] 0.013871 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005311 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019799 _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] 0.012128 _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 CA A 1 401 1 CA CA . C 3 GDP A 1 402 1 GDP GDP . D 4 9PC A 1 403 1 9PC PC1 . E 5 HOH A 1 501 1 HOH HOH . E 5 HOH A 2 502 2 HOH HOH . E 5 HOH A 3 503 3 HOH HOH . E 5 HOH A 4 504 4 HOH HOH . E 5 HOH A 5 505 5 HOH HOH . E 5 HOH A 6 506 6 HOH HOH . E 5 HOH A 7 507 7 HOH HOH . E 5 HOH A 8 508 8 HOH HOH . E 5 HOH A 9 509 9 HOH HOH . E 5 HOH A 10 510 10 HOH HOH . E 5 HOH A 11 511 11 HOH HOH . E 5 HOH A 12 512 12 HOH HOH . E 5 HOH A 13 513 13 HOH HOH . E 5 HOH A 14 514 14 HOH HOH . E 5 HOH A 15 515 15 HOH HOH . E 5 HOH A 16 516 16 HOH HOH . E 5 HOH A 17 517 17 HOH HOH . E 5 HOH A 18 518 18 HOH HOH . E 5 HOH A 19 519 19 HOH HOH . E 5 HOH A 20 520 20 HOH HOH . E 5 HOH A 21 521 21 HOH HOH . E 5 HOH A 22 522 22 HOH HOH . E 5 HOH A 23 523 23 HOH HOH . E 5 HOH A 24 524 24 HOH HOH . E 5 HOH A 25 525 25 HOH HOH . E 5 HOH A 26 526 26 HOH HOH . E 5 HOH A 27 527 27 HOH HOH . E 5 HOH A 28 528 28 HOH HOH . E 5 HOH A 29 529 29 HOH HOH . E 5 HOH A 30 530 30 HOH HOH . E 5 HOH A 31 531 31 HOH HOH . E 5 HOH A 32 532 32 HOH HOH . E 5 HOH A 33 533 33 HOH HOH . E 5 HOH A 34 534 34 HOH HOH . E 5 HOH A 35 535 35 HOH HOH . E 5 HOH A 36 536 36 HOH HOH . E 5 HOH A 37 537 37 HOH HOH . E 5 HOH A 38 538 38 HOH HOH . E 5 HOH A 39 539 39 HOH HOH . E 5 HOH A 40 540 40 HOH HOH . E 5 HOH A 41 541 41 HOH HOH . E 5 HOH A 42 542 42 HOH HOH . E 5 HOH A 43 543 43 HOH HOH . E 5 HOH A 44 544 44 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 . . . C 3 -21.138 -10.525 14.383 1 22.35 ? PB GDP 402 A 1 HETATM 2 O O1B GDP . . . C 3 -21.674 -11.714 13.628 1 22.77 ? O1B GDP 402 A 1 HETATM 3 O O2B GDP . . . C 3 -19.655 -10.405 14.125 1 23.24 ? O2B GDP 402 A 1 HETATM 4 O O3B GDP . . . C 3 -21.856 -9.249 13.998 1 17.96 ? O3B GDP 402 A 1 HETATM 5 O O3A GDP . . . C 3 -21.387 -10.877 15.92 1 24.75 ? O3A GDP 402 A 1 HETATM 6 P PA GDP . . . C 3 -21.007 -9.882 17.097 1 18.54 ? PA GDP 402 A 1 HETATM 7 O O1A GDP . . . C 3 -19.887 -8.925 16.734 1 19.3 ? O1A GDP 402 A 1 HETATM 8 O O2A GDP . . . C 3 -22.217 -9.1 17.529 1 22.32 ? O2A GDP 402 A 1 HETATM 9 O O5' GDP . . . C 3 -20.603 -11 18.173 1 17.96 ? O5' GDP 402 A 1 HETATM 10 C C5' GDP . . . C 3 -19.345 -11.67 18.097 1 20.24 ? C5' GDP 402 A 1 HETATM 11 C C4' GDP . . . C 3 -18.632 -11.656 19.442 1 17.81 ? C4' GDP 402 A 1 HETATM 12 O O4' GDP . . . C 3 -18.291 -10.314 19.777 1 17.65 ? O4' GDP 402 A 1 HETATM 13 C C3' GDP . . . C 3 -19.536 -12.161 20.554 1 18.52 ? C3' GDP 402 A 1 HETATM 14 O O3' GDP . . . C 3 -19.285 -13.55 20.799 1 18.95 ? O3' GDP 402 A 1 HETATM 15 C C2' GDP . . . C 3 -19.237 -11.264 21.749 1 17.99 ? C2' GDP 402 A 1 HETATM 16 O O2' GDP . . . C 3 -18.236 -11.827 22.6 1 21.1 ? O2' GDP 402 A 1 HETATM 17 C C1' GDP . . . C 3 -18.562 -10.048 21.16 1 18.91 ? C1' GDP 402 A 1 HETATM 18 N N9 GDP . . . C 3 -19.329 -8.782 21.299 1 17.43 ? N9 GDP 402 A 1 HETATM 19 C C8 GDP . . . C 3 -20.461 -8.421 20.676 1 18.23 ? C8 GDP 402 A 1 HETATM 20 N N7 GDP . . . C 3 -20.854 -7.17 21.028 1 17.63 ? N7 GDP 402 A 1 HETATM 21 C C5 GDP . . . C 3 -19.937 -6.7 21.896 1 20.52 ? C5 GDP 402 A 1 HETATM 22 C C6 GDP . . . C 3 -19.71 -5.445 22.668 1 22.92 ? C6 GDP 402 A 1 HETATM 23 O O6 GDP . . . C 3 -20.507 -4.482 22.583 1 27.95 ? O6 GDP 402 A 1 HETATM 24 N N1 GDP . . . C 3 -18.622 -5.383 23.454 1 20.59 ? N1 GDP 402 A 1 HETATM 25 C C2 GDP . . . C 3 -17.751 -6.409 23.561 1 20.69 ? C2 GDP 402 A 1 HETATM 26 N N2 GDP . . . C 3 -16.682 -6.279 24.377 1 17.51 ? N2 GDP 402 A 1 HETATM 27 N N3 GDP . . . C 3 -17.889 -7.575 22.888 1 17.2 ? N3 GDP 402 A 1 HETATM 28 C C4 GDP . . . C 3 -18.937 -7.769 22.059 1 18.26 ? C4 GDP 402 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #