data_4XCQ # _model_server_result.job_id uwyOj1YUC044V1adLTw7oA _model_server_result.datetime_utc '2025-03-05 19:38:54' _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 4xcq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4XCQ # _exptl.entry_id 4XCQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 92.49 _cell.angle_gamma 90 _cell.entry_id 4XCQ _cell.length_a 104.97 _cell.length_b 86.342 _cell.length_c 44.734 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XCQ _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id C _struct_conn.ptnr1_label_atom_id NA _struct_conn.ptnr1_label_comp_id NA _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id NA _struct_conn.ptnr1_auth_seq_id 402 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id O _struct_conn.ptnr2_label_comp_id HOH _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HOH _struct_conn.ptnr2_auth_seq_id 539 _struct_conn.ptnr2_symmetry 2_555 _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 3.135 _struct_conn.pdbx_value_order ? # _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 4XCQ _atom_sites.fract_transf_matrix[1][1] 0.009527 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000414 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011582 _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] 0.022376 _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 GDP A 1 401 1 GDP GDP . C 3 NA A 1 402 1 NA NA . D 4 HOH A 1 501 10 HOH HOH . D 4 HOH A 2 502 28 HOH HOH . D 4 HOH A 3 503 31 HOH HOH . D 4 HOH A 4 504 20 HOH HOH . D 4 HOH A 5 505 26 HOH HOH . D 4 HOH A 6 506 7 HOH HOH . D 4 HOH A 7 507 5 HOH HOH . D 4 HOH A 8 508 9 HOH HOH . D 4 HOH A 9 509 1 HOH HOH . D 4 HOH A 10 510 43 HOH HOH . D 4 HOH A 11 511 40 HOH HOH . D 4 HOH A 12 512 19 HOH HOH . D 4 HOH A 13 513 24 HOH HOH . D 4 HOH A 14 514 11 HOH HOH . D 4 HOH A 15 515 2 HOH HOH . D 4 HOH A 16 516 3 HOH HOH . D 4 HOH A 17 517 16 HOH HOH . D 4 HOH A 18 518 6 HOH HOH . D 4 HOH A 19 519 39 HOH HOH . D 4 HOH A 20 520 4 HOH HOH . D 4 HOH A 21 521 29 HOH HOH . D 4 HOH A 22 522 35 HOH HOH . D 4 HOH A 23 523 33 HOH HOH . D 4 HOH A 24 524 25 HOH HOH . D 4 HOH A 25 525 38 HOH HOH . D 4 HOH A 26 526 34 HOH HOH . D 4 HOH A 27 527 18 HOH HOH . D 4 HOH A 28 528 42 HOH HOH . D 4 HOH A 29 529 13 HOH HOH . D 4 HOH A 30 530 44 HOH HOH . D 4 HOH A 31 531 8 HOH HOH . D 4 HOH A 32 532 36 HOH HOH . D 4 HOH A 33 533 15 HOH HOH . D 4 HOH A 34 534 21 HOH HOH . D 4 HOH A 35 535 27 HOH HOH . D 4 HOH A 36 536 37 HOH HOH . D 4 HOH A 37 537 41 HOH HOH . D 4 HOH A 38 538 17 HOH HOH . D 4 HOH A 39 539 32 HOH HOH . D 4 HOH A 40 540 12 HOH HOH . D 4 HOH A 41 541 30 HOH HOH . D 4 HOH A 42 542 23 HOH HOH . D 4 HOH A 43 543 14 HOH HOH . D 4 HOH A 44 544 22 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 . . . B 2 17.053 1.893 17.55 1 39.12 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 17.621 1.637 16.17 1 48.46 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 17.645 0.904 18.533 1 32.45 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 15.548 1.754 17.535 1 33.47 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 17.455 3.366 18.025 1 36.16 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 17.007 4.688 17.234 1 48.92 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 16.032 5.521 18.028 1 55.35 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 16.466 4.375 15.856 1 51.76 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 18.441 5.397 17.132 1 57.89 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 18.805 6.467 17.989 1 54.52 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 19.854 7.251 17.227 1 58.38 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 19.427 7.312 15.864 1 57.94 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 19.944 8.669 17.746 1 52.18 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 21.253 8.856 18.279 1 56.04 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 19.717 9.562 16.542 1 54.76 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 20.974 10.099 16.122 1 56.49 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 19.203 8.657 15.437 1 53.4 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 17.743 8.775 15.175 1 54.15 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 16.775 8.254 15.958 1 51 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 15.54 8.494 15.454 1 47.85 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 15.708 9.175 14.305 1 50.43 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 14.813 9.74 13.269 1 45.76 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 13.571 9.62 13.37 1 41.7 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 15.372 10.379 12.231 1 42.75 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 16.707 10.518 12.109 1 42.49 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 17.189 11.18 11.027 1 39.22 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 17.586 10.025 13.023 1 39.07 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 17.158 9.355 14.12 1 49.33 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #