data_4DXD # _model_server_result.job_id 60es2Gehi80g8-sJT0xttw _model_server_result.datetime_utc '2025-07-15 08:54:47' _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 4dxd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4DXD # _exptl.entry_id 4DXD _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 106.75 _cell.angle_gamma 90 _cell.entry_id 4DXD _cell.length_a 67.715 _cell.length_b 54.65 _cell.length_c 84.496 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DXD _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 # _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 4DXD _atom_sites.fract_transf_matrix[1][1] 0.014768 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004445 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018298 _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] 0.012359 _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 1 401 500 GDP GDP . C 3 9PC A 1 402 512 9PC 723 . D 4 HOH A 1 501 1 HOH HOH . D 4 HOH A 2 502 2 HOH HOH . D 4 HOH A 3 503 3 HOH HOH . D 4 HOH A 4 504 4 HOH HOH . D 4 HOH A 5 505 5 HOH HOH . D 4 HOH A 6 506 6 HOH HOH . D 4 HOH A 7 507 7 HOH HOH . D 4 HOH A 8 508 8 HOH HOH . D 4 HOH A 9 509 9 HOH HOH . D 4 HOH A 10 510 10 HOH HOH . D 4 HOH A 11 511 11 HOH HOH . D 4 HOH A 12 512 12 HOH HOH . D 4 HOH A 13 513 13 HOH HOH . D 4 HOH A 14 514 14 HOH HOH . D 4 HOH A 15 515 15 HOH HOH . D 4 HOH A 16 516 16 HOH HOH . D 4 HOH A 17 517 17 HOH HOH . D 4 HOH A 18 518 18 HOH HOH . D 4 HOH A 19 519 19 HOH HOH . D 4 HOH A 20 520 20 HOH HOH . D 4 HOH A 21 521 21 HOH HOH . D 4 HOH A 22 522 22 HOH HOH . D 4 HOH A 23 523 23 HOH HOH . D 4 HOH A 24 524 24 HOH HOH . D 4 HOH A 25 525 25 HOH HOH . D 4 HOH A 26 526 26 HOH HOH . D 4 HOH A 27 527 27 HOH HOH . D 4 HOH A 28 528 28 HOH HOH . D 4 HOH A 29 529 29 HOH HOH . D 4 HOH A 30 530 30 HOH HOH . D 4 HOH A 31 531 31 HOH HOH . D 4 HOH A 32 532 32 HOH HOH . D 4 HOH A 33 533 33 HOH HOH . D 4 HOH A 34 534 34 HOH HOH . D 4 HOH A 35 535 35 HOH HOH . D 4 HOH A 36 536 36 HOH HOH . D 4 HOH A 37 537 37 HOH HOH . D 4 HOH A 38 538 38 HOH HOH . D 4 HOH A 39 539 39 HOH HOH . D 4 HOH A 40 540 40 HOH HOH . D 4 HOH A 41 541 41 HOH HOH . D 4 HOH A 42 542 42 HOH HOH . D 4 HOH A 43 543 43 HOH HOH . D 4 HOH A 44 544 44 HOH HOH . D 4 HOH A 45 545 45 HOH HOH . D 4 HOH A 46 546 46 HOH HOH . D 4 HOH A 47 547 47 HOH HOH . D 4 HOH A 48 548 48 HOH HOH . D 4 HOH A 49 549 49 HOH HOH . D 4 HOH A 50 550 50 HOH HOH . D 4 HOH A 51 551 51 HOH HOH . D 4 HOH A 52 552 52 HOH HOH . D 4 HOH A 53 553 53 HOH HOH . D 4 HOH A 54 554 54 HOH HOH . D 4 HOH A 55 555 55 HOH HOH . D 4 HOH A 56 556 56 HOH HOH . D 4 HOH A 57 557 57 HOH HOH . D 4 HOH A 58 558 58 HOH HOH . D 4 HOH A 59 559 59 HOH HOH . D 4 HOH A 60 560 60 HOH HOH . D 4 HOH A 61 561 61 HOH HOH . D 4 HOH A 62 562 62 HOH HOH . D 4 HOH A 63 563 63 HOH HOH . D 4 HOH A 64 564 64 HOH HOH . D 4 HOH A 65 565 65 HOH HOH . D 4 HOH A 66 566 66 HOH HOH . D 4 HOH A 67 567 67 HOH HOH . D 4 HOH A 68 568 68 HOH HOH . D 4 HOH A 69 569 69 HOH HOH . D 4 HOH A 70 570 70 HOH HOH . D 4 HOH A 71 571 71 HOH HOH . D 4 HOH A 72 572 72 HOH HOH . D 4 HOH A 73 573 73 HOH HOH . D 4 HOH A 74 574 74 HOH HOH . D 4 HOH A 75 575 75 HOH HOH . D 4 HOH A 76 576 76 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 6.683 19.058 26.655 1 29.84 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 7.648 20.28 26.838 1 30.53 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 5.245 19.332 27.221 1 31.9 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 7.042 17.903 27.43 1 32.6 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 6.454 18.512 25.139 1 27.9 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 6.342 19.469 23.884 1 26.85 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 7.657 19.908 23.434 1 28.04 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 5.497 20.823 24.101 1 28.7 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 5.77 18.478 22.806 1 26.87 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 4.509 17.935 23.06 1 26.42 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 3.793 17.846 21.689 1 27.04 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 3.661 19.184 21.191 1 26.53 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 4.73 17.169 20.605 1 27.81 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 4.345 15.818 20.736 1 32.26 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 4.259 17.818 19.258 1 28 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 3.007 17.305 18.866 1 29.92 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 3.879 19.219 19.724 1 26.35 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 4.717 20.382 19.503 1 25.15 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 5.897 20.74 20.105 1 24.86 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 6.318 21.901 19.669 1 24.97 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 5.37 22.409 18.826 1 23.89 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 5.179 23.604 18.089 1 24.89 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 5.971 24.498 18.099 1 24.97 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 4.078 23.736 17.332 1 24.53 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 3.116 22.789 17.237 1 24.73 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 2.011 23.048 16.401 1 26.68 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 3.257 21.65 17.898 1 25.02 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 4.331 21.427 18.696 1 24.61 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #