data_5CIW # _model_server_result.job_id TWYFNusNcZwqcVkjTSFMng _model_server_result.datetime_utc '2025-03-04 07:39:48' _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 5ciw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5CIW # _exptl.entry_id 5CIW _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.55 _cell.angle_gamma 90 _cell.entry_id 5CIW _cell.length_a 57.9 _cell.length_b 59.33 _cell.length_c 64.79 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CIW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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,G 1 1 B,E,F,H 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 ? 2 C N N ? 2 F 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 OG1 THR 24 A THR 24 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc2 C O2B GDP . A GDP 301 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc3 D MG MG . A MG 302 1_555 G O HOH . A HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc4 D MG MG . A MG 302 1_555 G O HOH . A HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc5 D MG MG . A MG 302 1_555 G O HOH . A HOH 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc6 D MG MG . A MG 302 1_555 G O HOH . A HOH 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc7 B OG1 THR 24 B THR 24 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc8 E MG MG . B MG 301 1_555 F O2B GDP . B GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc9 E MG MG . B MG 301 1_555 H O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc10 E MG MG . B MG 301 1_555 H O HOH . B HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc11 E MG MG . B MG 301 1_555 H O HOH . B HOH 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc12 E MG MG . B MG 301 1_555 H O HOH . B HOH 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? # _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 5CIW _atom_sites.fract_transf_matrix[1][1] 0.017271 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001984 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016855 _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] 0.015536 _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 GDP A 1 301 301 GDP GDP . D 3 MG A 1 302 302 MG MG . E 3 MG B 1 301 302 MG MG . F 2 GDP B 1 302 301 GDP GDP . G 4 HOH A 1 401 112 HOH HOH . G 4 HOH A 2 402 90 HOH HOH . G 4 HOH A 3 403 85 HOH HOH . G 4 HOH A 4 404 46 HOH HOH . G 4 HOH A 5 405 10 HOH HOH . G 4 HOH A 6 406 94 HOH HOH . G 4 HOH A 7 407 88 HOH HOH . G 4 HOH A 8 408 106 HOH HOH . G 4 HOH A 9 409 108 HOH HOH . G 4 HOH A 10 410 65 HOH HOH . G 4 HOH A 11 411 111 HOH HOH . G 4 HOH A 12 412 9 HOH HOH . G 4 HOH A 13 413 23 HOH HOH . G 4 HOH A 14 414 16 HOH HOH . G 4 HOH A 15 415 69 HOH HOH . G 4 HOH A 16 416 8 HOH HOH . G 4 HOH A 17 417 49 HOH HOH . G 4 HOH A 18 418 105 HOH HOH . G 4 HOH A 19 419 91 HOH HOH . G 4 HOH A 20 420 80 HOH HOH . G 4 HOH A 21 421 19 HOH HOH . G 4 HOH A 22 422 40 HOH HOH . G 4 HOH A 23 423 3 HOH HOH . G 4 HOH A 24 424 24 HOH HOH . G 4 HOH A 25 425 36 HOH HOH . G 4 HOH A 26 426 50 HOH HOH . G 4 HOH A 27 427 15 HOH HOH . G 4 HOH A 28 428 70 HOH HOH . G 4 HOH A 29 429 26 HOH HOH . G 4 HOH A 30 430 75 HOH HOH . G 4 HOH A 31 431 83 HOH HOH . G 4 HOH A 32 432 64 HOH HOH . G 4 HOH A 33 433 53 HOH HOH . G 4 HOH A 34 434 20 HOH HOH . G 4 HOH A 35 435 5 HOH HOH . G 4 HOH A 36 436 21 HOH HOH . G 4 HOH A 37 437 58 HOH HOH . G 4 HOH A 38 438 41 HOH HOH . G 4 HOH A 39 439 14 HOH HOH . G 4 HOH A 40 440 25 HOH HOH . G 4 HOH A 41 441 110 HOH HOH . G 4 HOH A 42 442 68 HOH HOH . G 4 HOH A 43 443 63 HOH HOH . G 4 HOH A 44 444 71 HOH HOH . G 4 HOH A 45 445 54 HOH HOH . G 4 HOH A 46 446 18 HOH HOH . G 4 HOH A 47 447 100 HOH HOH . G 4 HOH A 48 448 13 HOH HOH . G 4 HOH A 49 449 45 HOH HOH . G 4 HOH A 50 450 17 HOH HOH . G 4 HOH A 51 451 55 HOH HOH . G 4 HOH A 52 452 87 HOH HOH . G 4 HOH A 53 453 73 HOH HOH . G 4 HOH A 54 454 42 HOH HOH . G 4 HOH A 55 455 60 HOH HOH . G 4 HOH A 56 456 74 HOH HOH . G 4 HOH A 57 457 1 HOH HOH . G 4 HOH A 58 458 95 HOH HOH . G 4 HOH A 59 459 93 HOH HOH . G 4 HOH A 60 460 52 HOH HOH . G 4 HOH A 61 461 82 HOH HOH . G 4 HOH A 62 462 89 HOH HOH . G 4 HOH A 63 463 103 HOH HOH . G 4 HOH A 64 464 47 HOH HOH . G 4 HOH A 65 465 59 HOH HOH . G 4 HOH A 66 466 98 HOH HOH . G 4 HOH A 67 467 57 HOH HOH . G 4 HOH A 68 468 96 HOH HOH . G 4 HOH A 69 469 22 HOH HOH . G 4 HOH A 70 470 97 HOH HOH . H 4 HOH B 1 401 113 HOH HOH . H 4 HOH B 2 402 86 HOH HOH . H 4 HOH B 3 403 62 HOH HOH . H 4 HOH B 4 404 33 HOH HOH . H 4 HOH B 5 405 72 HOH HOH . H 4 HOH B 6 406 99 HOH HOH . H 4 HOH B 7 407 84 HOH HOH . H 4 HOH B 8 408 27 HOH HOH . H 4 HOH B 9 409 35 HOH HOH . H 4 HOH B 10 410 67 HOH HOH . H 4 HOH B 11 411 79 HOH HOH . H 4 HOH B 12 412 7 HOH HOH . H 4 HOH B 13 413 30 HOH HOH . H 4 HOH B 14 414 76 HOH HOH . H 4 HOH B 15 415 56 HOH HOH . H 4 HOH B 16 416 61 HOH HOH . H 4 HOH B 17 417 102 HOH HOH . H 4 HOH B 18 418 4 HOH HOH . H 4 HOH B 19 419 44 HOH HOH . H 4 HOH B 20 420 11 HOH HOH . H 4 HOH B 21 421 66 HOH HOH . H 4 HOH B 22 422 77 HOH HOH . H 4 HOH B 23 423 107 HOH HOH . H 4 HOH B 24 424 51 HOH HOH . H 4 HOH B 25 425 43 HOH HOH . H 4 HOH B 26 426 38 HOH HOH . H 4 HOH B 27 427 31 HOH HOH . H 4 HOH B 28 428 2 HOH HOH . H 4 HOH B 29 429 6 HOH HOH . H 4 HOH B 30 430 12 HOH HOH . H 4 HOH B 31 431 48 HOH HOH . H 4 HOH B 32 432 109 HOH HOH . H 4 HOH B 33 433 28 HOH HOH . H 4 HOH B 34 434 37 HOH HOH . H 4 HOH B 35 435 81 HOH HOH . H 4 HOH B 36 436 32 HOH HOH . H 4 HOH B 37 437 39 HOH HOH . H 4 HOH B 38 438 29 HOH HOH . H 4 HOH B 39 439 104 HOH HOH . H 4 HOH B 40 440 101 HOH HOH . H 4 HOH B 41 441 34 HOH HOH . H 4 HOH B 42 442 78 HOH HOH . H 4 HOH B 43 443 92 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 2 -24.804 -5.22 -6.5 1 20.22 ? PB GDP 301 A 1 HETATM 2 O O1B GDP . . . C 2 -24.867 -3.966 -7.298 1 18.64 ? O1B GDP 301 A 1 HETATM 3 O O2B GDP . . . C 2 -24.648 -5.017 -5.01 1 19.67 ? O2B GDP 301 A 1 HETATM 4 O O3B GDP . . . C 2 -25.843 -6.275 -6.86 1 22.96 ? O3B GDP 301 A 1 HETATM 5 O O3A GDP . . . C 2 -23.456 -5.95 -7.035 1 19.05 ? O3A GDP 301 A 1 HETATM 6 P PA GDP . . . C 2 -22.447 -6.917 -6.321 1 19.3 ? PA GDP 301 A 1 HETATM 7 O O1A GDP . . . C 2 -22.992 -8.062 -5.549 1 19.12 ? O1A GDP 301 A 1 HETATM 8 O O2A GDP . . . C 2 -21.478 -6.119 -5.514 1 19.64 ? O2A GDP 301 A 1 HETATM 9 O O5' GDP . . . C 2 -21.464 -7.432 -7.54 1 19.82 ? O5' GDP 301 A 1 HETATM 10 C C5' GDP . . . C 2 -22.153 -8.236 -8.514 1 21.81 ? C5' GDP 301 A 1 HETATM 11 C C4' GDP . . . C 2 -21.056 -8.939 -9.284 1 20.96 ? C4' GDP 301 A 1 HETATM 12 O O4' GDP . . . C 2 -20.137 -8.043 -9.937 1 21.51 ? O4' GDP 301 A 1 HETATM 13 C C3' GDP . . . C 2 -20.266 -9.852 -8.369 1 22.45 ? C3' GDP 301 A 1 HETATM 14 O O3' GDP . . . C 2 -19.953 -11.044 -9.137 1 27.77 ? O3' GDP 301 A 1 HETATM 15 C C2' GDP . . . C 2 -18.978 -9.099 -8.224 1 20.86 ? C2' GDP 301 A 1 HETATM 16 O O2' GDP . . . C 2 -17.889 -9.885 -7.802 1 23.42 ? O2' GDP 301 A 1 HETATM 17 C C1' GDP . . . C 2 -18.842 -8.432 -9.595 1 22.47 ? C1' GDP 301 A 1 HETATM 18 N N9 GDP . . . C 2 -18.159 -7.162 -9.454 1 21.34 ? N9 GDP 301 A 1 HETATM 19 C C8 GDP . . . C 2 -18.492 -6.154 -8.613 1 19.37 ? C8 GDP 301 A 1 HETATM 20 N N7 GDP . . . C 2 -17.646 -5.152 -8.771 1 18.37 ? N7 GDP 301 A 1 HETATM 21 C C5 GDP . . . C 2 -16.739 -5.471 -9.733 1 19.37 ? C5 GDP 301 A 1 HETATM 22 C C6 GDP . . . C 2 -15.556 -4.827 -10.357 1 21.23 ? C6 GDP 301 A 1 HETATM 23 O O6 GDP . . . C 2 -15.112 -3.679 -10.086 1 18.51 ? O6 GDP 301 A 1 HETATM 24 N N1 GDP . . . C 2 -14.883 -5.55 -11.319 1 20.38 ? N1 GDP 301 A 1 HETATM 25 C C2 GDP . . . C 2 -15.319 -6.777 -11.669 1 21.46 ? C2 GDP 301 A 1 HETATM 26 N N2 GDP . . . C 2 -14.61 -7.407 -12.627 1 20.33 ? N2 GDP 301 A 1 HETATM 27 N N3 GDP . . . C 2 -16.328 -7.426 -11.099 1 21.6 ? N3 GDP 301 A 1 HETATM 28 C C4 GDP . . . C 2 -17.108 -6.817 -10.165 1 20.72 ? C4 GDP 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #