data_3X1W # _model_server_result.job_id JOfeObvzFYl8M0SbbwiiZQ _model_server_result.datetime_utc '2024-11-15 09:55:21' _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 3x1w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 3X1W # _exptl.entry_id 3X1W _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 90 _cell.angle_gamma 90 _cell.entry_id 3X1W _cell.length_a 43.529 _cell.length_b 52.433 _cell.length_c 60.548 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3X1W _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 118 A CYS 118 1_555 A SG CYS 141 A CYS 141 4_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc1 A OG SER 17 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc2 A OE1 GLU 156 A GLU 156 1_555 D CD CD . A CD 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc3 A OD1 ASP 160 A ASP 160 1_555 D CD CD . A CD 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc4 A OD2 ASP 160 A ASP 160 1_555 D CD CD . A CD 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc5 B O2B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc7 C MG MG . A MG 202 1_555 E O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc8 C MG MG . A MG 202 1_555 E O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc9 C MG MG . A MG 202 1_555 E O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc10 D CD CD . A CD 203 1_555 E O HOH . A HOH 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc11 D CD CD . A CD 203 1_555 E O HOH . A HOH 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? # _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 3X1W _atom_sites.fract_transf_matrix[1][1] 0.022973 _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] 0.019072 _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] 0.016516 _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 1 201 1 GDP GDP . C 3 MG A 1 202 1 MG MG . D 4 CD A 1 203 1 CD CD . E 5 HOH A 1 301 1 HOH HOH . E 5 HOH A 2 302 2 HOH HOH . E 5 HOH A 3 303 3 HOH HOH . E 5 HOH A 4 304 4 HOH HOH . E 5 HOH A 5 305 5 HOH HOH . E 5 HOH A 6 306 6 HOH HOH . E 5 HOH A 7 307 7 HOH HOH . E 5 HOH A 8 308 8 HOH HOH . E 5 HOH A 9 309 9 HOH HOH . E 5 HOH A 10 310 10 HOH HOH . E 5 HOH A 11 311 11 HOH HOH . E 5 HOH A 12 312 12 HOH HOH . E 5 HOH A 13 313 13 HOH HOH . E 5 HOH A 14 314 14 HOH HOH . E 5 HOH A 15 315 15 HOH HOH . E 5 HOH A 16 316 16 HOH HOH . E 5 HOH A 17 317 17 HOH HOH . E 5 HOH A 18 318 18 HOH HOH . E 5 HOH A 19 319 19 HOH HOH . E 5 HOH A 20 320 20 HOH HOH . E 5 HOH A 21 321 21 HOH HOH . E 5 HOH A 22 322 22 HOH HOH . E 5 HOH A 23 323 23 HOH HOH . E 5 HOH A 24 324 24 HOH HOH . E 5 HOH A 25 325 25 HOH HOH . E 5 HOH A 26 326 26 HOH HOH . E 5 HOH A 27 327 27 HOH HOH . E 5 HOH A 28 328 28 HOH HOH . E 5 HOH A 29 329 29 HOH HOH . E 5 HOH A 30 330 30 HOH HOH . E 5 HOH A 31 331 31 HOH HOH . E 5 HOH A 32 332 32 HOH HOH . E 5 HOH A 33 333 33 HOH HOH . E 5 HOH A 34 334 34 HOH HOH . E 5 HOH A 35 335 35 HOH HOH . E 5 HOH A 36 336 36 HOH HOH . E 5 HOH A 37 337 37 HOH HOH . E 5 HOH A 38 338 38 HOH HOH . E 5 HOH A 39 339 39 HOH HOH . E 5 HOH A 40 340 40 HOH HOH . E 5 HOH A 41 341 41 HOH HOH . E 5 HOH A 42 342 42 HOH HOH . E 5 HOH A 43 343 43 HOH HOH . E 5 HOH A 44 344 44 HOH HOH . E 5 HOH A 45 345 45 HOH HOH . E 5 HOH A 46 346 46 HOH HOH . E 5 HOH A 47 347 47 HOH HOH . E 5 HOH A 48 348 48 HOH HOH . E 5 HOH A 49 349 49 HOH HOH . E 5 HOH A 50 350 50 HOH HOH . E 5 HOH A 51 351 51 HOH HOH . E 5 HOH A 52 352 52 HOH HOH . E 5 HOH A 53 353 53 HOH HOH . E 5 HOH A 54 354 54 HOH HOH . E 5 HOH A 55 355 55 HOH HOH . E 5 HOH A 56 356 56 HOH HOH . E 5 HOH A 57 357 57 HOH HOH . E 5 HOH A 58 358 58 HOH HOH . E 5 HOH A 59 359 59 HOH HOH . E 5 HOH A 60 360 60 HOH HOH . E 5 HOH A 61 361 61 HOH HOH . E 5 HOH A 62 362 62 HOH HOH . E 5 HOH A 63 363 63 HOH HOH . E 5 HOH A 64 364 64 HOH HOH . E 5 HOH A 65 365 65 HOH HOH . E 5 HOH A 66 366 66 HOH HOH . E 5 HOH A 67 367 67 HOH HOH . E 5 HOH A 68 368 68 HOH HOH . E 5 HOH A 69 369 69 HOH HOH . E 5 HOH A 70 370 70 HOH HOH . E 5 HOH A 71 371 71 HOH HOH . E 5 HOH A 72 372 72 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 -11.457 4.8 -6.55 1 8.69 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -11.61 5.605 -7.825 1 9.87 -1 O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -11.135 5.673 -5.35 1 8.85 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -10.439 3.689 -6.748 1 8.27 -1 O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -12.852 4.078 -6.3 1 9.14 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -14.024 4.458 -5.296 1 9.8 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -14.43 5.884 -5.55 1 13.2 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -13.669 4.141 -3.858 1 10.98 -1 O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -15.188 3.467 -5.704 1 8.76 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -15.755 3.512 -7.017 1 9.8 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -17.112 2.905 -7.055 1 10.55 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -16.989 1.442 -6.725 1 11.24 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -18.013 3.494 -6.061 1 11.61 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -19.352 3.492 -6.619 1 13.36 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -17.92 2.608 -4.906 1 11.75 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -19.106 2.649 -4.08 1 13.89 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -17.748 1.253 -5.447 1 10.91 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -17.029 0.356 -4.653 1 9.95 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -15.881 0.575 -4.112 1 8.99 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -15.499 -0.537 -3.478 1 9.74 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -16.489 -1.5 -3.675 1 9.45 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -16.683 -2.896 -3.278 1 10.51 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -15.874 -3.514 -2.575 1 10.92 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -17.838 -3.528 -3.695 1 10.26 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -18.811 -2.848 -4.493 1 11.77 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -19.958 -3.559 -4.895 1 14 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -18.647 -1.567 -4.88 1 10.61 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -17.462 -0.863 -4.473 1 9.46 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #