data_7ODN # _model_server_result.job_id 2w8F8aHuJaN1tXFjCEpuhg _model_server_result.datetime_utc '2024-11-06 01:57:11' _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 7odn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 7ODN # _exptl.entry_id 7ODN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 8 _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 97.23 _cell.angle_gamma 90 _cell.entry_id 7ODN _cell.length_a 73.441 _cell.length_b 91.39 _cell.length_c 82.671 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ODN _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S _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 8 _struct_asym.id I _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 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc2 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc3 E MG MG . A MG 502 1_555 Q O HOH . A HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc4 E MG MG . A MG 502 1_555 Q O HOH . A HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc5 E MG MG . A MG 502 1_555 Q O HOH . A HOH 628 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc6 E MG MG . A MG 502 1_555 Q O HOH . A HOH 638 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? # _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 7ODN _atom_sites.fract_transf_matrix[1][1] 0.013616 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001728 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010942 _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] 0.012193 _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 D 4 GTP A 1 501 500 GTP GTP . E 5 MG A 1 502 501 MG MG . F 6 SO4 A 1 503 502 SO4 SO4 . G 7 CL A 1 504 503 CL CL . H 6 SO4 A 1 505 501 SO4 SO4 . I 8 GDP B 1 501 500 GDP GDP . J 9 V95 B 1 502 502 V95 MBZ . K 6 SO4 B 1 503 503 SO4 SO4 . L 6 SO4 B 1 504 504 SO4 SO4 . M 7 CL B 1 505 506 CL CL . N 10 GOL F 1 201 505 GOL GOL . O 6 SO4 F 1 202 500 SO4 SO4 . P 10 GOL F 1 203 501 GOL GOL . Q 11 HOH A 1 601 4 HOH HOH . Q 11 HOH A 2 602 97 HOH HOH . Q 11 HOH A 3 603 7 HOH HOH . Q 11 HOH A 4 604 9 HOH HOH . Q 11 HOH A 5 605 99 HOH HOH . Q 11 HOH A 6 606 15 HOH HOH . Q 11 HOH A 7 607 6 HOH HOH . Q 11 HOH A 8 608 81 HOH HOH . Q 11 HOH A 9 609 20 HOH HOH . Q 11 HOH A 10 610 1 HOH HOH . Q 11 HOH A 11 611 76 HOH HOH . Q 11 HOH A 12 612 102 HOH HOH . Q 11 HOH A 13 613 31 HOH HOH . Q 11 HOH A 14 614 14 HOH HOH . Q 11 HOH A 15 615 38 HOH HOH . Q 11 HOH A 16 616 27 HOH HOH . Q 11 HOH A 17 617 12 HOH HOH . Q 11 HOH A 18 618 60 HOH HOH . Q 11 HOH A 19 619 69 HOH HOH . Q 11 HOH A 20 620 18 HOH HOH . Q 11 HOH A 21 621 70 HOH HOH . Q 11 HOH A 22 622 101 HOH HOH . Q 11 HOH A 23 623 79 HOH HOH . Q 11 HOH A 24 624 62 HOH HOH . Q 11 HOH A 25 625 41 HOH HOH . Q 11 HOH A 26 626 35 HOH HOH . Q 11 HOH A 27 627 80 HOH HOH . Q 11 HOH A 28 628 13 HOH HOH . Q 11 HOH A 29 629 55 HOH HOH . Q 11 HOH A 30 630 40 HOH HOH . Q 11 HOH A 31 631 58 HOH HOH . Q 11 HOH A 32 632 71 HOH HOH . Q 11 HOH A 33 633 21 HOH HOH . Q 11 HOH A 34 634 3 HOH HOH . Q 11 HOH A 35 635 75 HOH HOH . Q 11 HOH A 36 636 34 HOH HOH . Q 11 HOH A 37 637 106 HOH HOH . Q 11 HOH A 38 638 8 HOH HOH . Q 11 HOH A 39 639 19 HOH HOH . Q 11 HOH A 40 640 37 HOH HOH . Q 11 HOH A 41 641 25 HOH HOH . Q 11 HOH A 42 642 49 HOH HOH . Q 11 HOH A 43 643 28 HOH HOH . Q 11 HOH A 44 644 63 HOH HOH . Q 11 HOH A 45 645 64 HOH HOH . Q 11 HOH A 46 646 65 HOH HOH . Q 11 HOH A 47 647 30 HOH HOH . Q 11 HOH A 48 648 94 HOH HOH . Q 11 HOH A 49 649 107 HOH HOH . Q 11 HOH A 50 650 59 HOH HOH . Q 11 HOH A 51 651 44 HOH HOH . Q 11 HOH A 52 652 24 HOH HOH . Q 11 HOH A 53 653 50 HOH HOH . Q 11 HOH A 54 654 68 HOH HOH . Q 11 HOH A 55 655 84 HOH HOH . Q 11 HOH A 56 656 89 HOH HOH . R 11 HOH B 1 601 56 HOH HOH . R 11 HOH B 2 602 2 HOH HOH . R 11 HOH B 3 603 98 HOH HOH . R 11 HOH B 4 604 96 HOH HOH . R 11 HOH B 5 605 91 HOH HOH . R 11 HOH B 6 606 32 HOH HOH . R 11 HOH B 7 607 78 HOH HOH . R 11 HOH B 8 608 22 HOH HOH . R 11 HOH B 9 609 100 HOH HOH . R 11 HOH B 10 610 72 HOH HOH . R 11 HOH B 11 611 51 HOH HOH . R 11 HOH B 12 612 93 HOH HOH . R 11 HOH B 13 613 16 HOH HOH . R 11 HOH B 14 614 104 HOH HOH . R 11 HOH B 15 615 85 HOH HOH . R 11 HOH B 16 616 23 HOH HOH . R 11 HOH B 17 617 46 HOH HOH . R 11 HOH B 18 618 74 HOH HOH . R 11 HOH B 19 619 108 HOH HOH . R 11 HOH B 20 620 95 HOH HOH . R 11 HOH B 21 621 109 HOH HOH . R 11 HOH B 22 622 73 HOH HOH . R 11 HOH B 23 623 86 HOH HOH . R 11 HOH B 24 624 90 HOH HOH . R 11 HOH B 25 625 83 HOH HOH . S 11 HOH F 1 301 105 HOH HOH . S 11 HOH F 2 302 10 HOH HOH . S 11 HOH F 3 303 29 HOH HOH . S 11 HOH F 4 304 26 HOH HOH . S 11 HOH F 5 305 43 HOH HOH . S 11 HOH F 6 306 61 HOH HOH . S 11 HOH F 7 307 42 HOH HOH . S 11 HOH F 8 308 36 HOH HOH . S 11 HOH F 9 309 48 HOH HOH . S 11 HOH F 10 310 67 HOH HOH . S 11 HOH F 11 311 11 HOH HOH . S 11 HOH F 12 312 66 HOH HOH . S 11 HOH F 13 313 33 HOH HOH . S 11 HOH F 14 314 17 HOH HOH . S 11 HOH F 15 315 39 HOH HOH . S 11 HOH F 16 316 103 HOH HOH . S 11 HOH F 17 317 5 HOH HOH . S 11 HOH F 18 318 88 HOH HOH . S 11 HOH F 19 319 47 HOH HOH . S 11 HOH F 20 320 52 HOH HOH . S 11 HOH F 21 321 92 HOH HOH . S 11 HOH F 22 322 45 HOH HOH . S 11 HOH F 23 323 54 HOH HOH . S 11 HOH F 24 324 77 HOH HOH . S 11 HOH F 25 325 53 HOH HOH . S 11 HOH F 26 326 82 HOH HOH . S 11 HOH F 27 327 57 HOH HOH . S 11 HOH F 28 328 87 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 . . . I 8 4.438 8.039 51.118 1 46.38 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . I 8 5.378 8.807 50.214 1 45.19 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . I 8 4.95 6.637 51.347 1 45.59 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . I 8 4.31 8.782 52.423 1 45.97 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . I 8 2.981 7.982 50.457 1 47.82 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . I 8 2.679 7.089 49.156 1 46.55 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . I 8 3.938 6.902 48.345 1 45.8 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . I 8 2.049 5.756 49.476 1 49.26 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . I 8 1.646 8.07 48.4 1 47.59 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . I 8 0.365 7.623 47.978 1 48.14 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . I 8 0.185 7.968 46.511 1 47.98 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . I 8 1.193 7.282 45.77 1 44.55 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . I 8 -1.149 7.486 45.977 1 49 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . I 8 -1.611 8.364 44.954 1 51.44 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . I 8 -0.857 6.124 45.383 1 46.11 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . I 8 -1.722 5.827 44.296 1 49.68 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . I 8 0.6 6.259 44.957 1 45.81 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . I 8 1.309 4.976 45.136 1 46.37 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . I 8 1.628 4.401 46.311 1 48.94 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . I 8 2.279 3.226 46.103 1 46.48 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . I 8 2.38 3.044 44.774 1 46.26 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . I 8 2.951 2.023 43.868 1 48.47 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . I 8 3.525 0.996 44.283 1 53 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . I 8 2.841 2.221 42.557 1 48.04 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . I 8 2.238 3.302 42.033 1 46.2 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . I 8 2.174 3.412 40.683 1 44.33 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . I 8 1.695 4.281 42.794 1 43.87 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . I 8 1.737 4.202 44.142 1 45.4 ? C4 GDP 501 B 1 HETATM 29 H H4' GDP . . . I 8 0.248 9.06 46.408 1 47.98 ? H4' GDP 501 B 1 HETATM 30 H H3' GDP . . . I 8 -1.924 7.453 46.755 1 49 ? H3' GDP 501 B 1 HETATM 31 H HO3' GDP . . . I 8 -2.501 8.101 44.681 1 51.44 ? HO3' GDP 501 B 1 HETATM 32 H H2' GDP . . . I 8 -1.026 5.289 46.077 1 46.11 ? H2' GDP 501 B 1 HETATM 33 H HO2' GDP . . . I 8 -2.568 5.505 44.635 1 49.68 ? HO2' GDP 501 B 1 HETATM 34 H H1' GDP . . . I 8 0.654 6.529 43.892 1 45.81 ? H1' GDP 501 B 1 HETATM 35 H H8 GDP . . . I 8 1.399 4.816 47.285 1 48.94 ? H8 GDP 501 B 1 HETATM 36 H HN1 GDP . . . I 8 3.237 1.509 41.91 1 48.04 ? HN1 GDP 501 B 1 HETATM 37 H HN21 GDP . . . I 8 2.573 2.692 40.097 1 44.33 ? HN21 GDP 501 B 1 HETATM 38 H HN22 GDP . . . I 8 1.73 4.214 40.264 1 44.33 ? HN22 GDP 501 B 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #