data_6UPR # _model_server_result.job_id UYBXAC1QhRczQfrEMQ0Ebw _model_server_result.datetime_utc '2024-11-05 04:01:17' _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 6upr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1401}' # _entry.id 6UPR # _exptl.entry_id 6UPR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 103.63 _cell.angle_gamma 90 _cell.entry_id 6UPR _cell.length_a 52.754 _cell.length_b 82.773 _cell.length_c 78.144 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6UPR _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _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 77 A CYS 111 1_555 A SG CYS 80 A CYS 114 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.037 ? metalc ? metalc1 B OG SER 39 B SER 58 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc2 D O1G GTP . B GTP 401 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc3 D O1B GTP . B GTP 401 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc4 E MG MG . B MG 402 1_555 G O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc5 E MG MG . B MG 402 1_555 G O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc6 E MG MG . B MG 402 1_555 G O HOH . B HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? # _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 6UPR _atom_sites.fract_transf_matrix[1][1] 0.018956 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004597 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012081 _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] 0.013168 _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 3 GDP A 1 1401 1401 GDP GDP . D 4 GTP B 1 401 500 GTP GTP . E 5 MG B 1 402 601 MG MG . F 6 HOH A 1 1501 66 HOH HOH . F 6 HOH A 2 1502 47 HOH HOH . F 6 HOH A 3 1503 50 HOH HOH . F 6 HOH A 4 1504 91 HOH HOH . F 6 HOH A 5 1505 30 HOH HOH . F 6 HOH A 6 1506 46 HOH HOH . F 6 HOH A 7 1507 39 HOH HOH . F 6 HOH A 8 1508 1 HOH HOH . F 6 HOH A 9 1509 72 HOH HOH . F 6 HOH A 10 1510 92 HOH HOH . F 6 HOH A 11 1511 4 HOH HOH . F 6 HOH A 12 1512 18 HOH HOH . F 6 HOH A 13 1513 13 HOH HOH . F 6 HOH A 14 1514 12 HOH HOH . F 6 HOH A 15 1515 3 HOH HOH . F 6 HOH A 16 1516 85 HOH HOH . F 6 HOH A 17 1517 57 HOH HOH . F 6 HOH A 18 1518 86 HOH HOH . F 6 HOH A 19 1519 21 HOH HOH . F 6 HOH A 20 1520 58 HOH HOH . F 6 HOH A 21 1521 2 HOH HOH . F 6 HOH A 22 1522 51 HOH HOH . F 6 HOH A 23 1523 36 HOH HOH . F 6 HOH A 24 1524 73 HOH HOH . F 6 HOH A 25 1525 33 HOH HOH . F 6 HOH A 26 1526 6 HOH HOH . F 6 HOH A 27 1527 45 HOH HOH . F 6 HOH A 28 1528 15 HOH HOH . F 6 HOH A 29 1529 41 HOH HOH . F 6 HOH A 30 1530 9 HOH HOH . F 6 HOH A 31 1531 24 HOH HOH . F 6 HOH A 32 1532 74 HOH HOH . F 6 HOH A 33 1533 5 HOH HOH . F 6 HOH A 34 1534 27 HOH HOH . F 6 HOH A 35 1535 11 HOH HOH . F 6 HOH A 36 1536 19 HOH HOH . F 6 HOH A 37 1537 78 HOH HOH . F 6 HOH A 38 1538 32 HOH HOH . F 6 HOH A 39 1539 67 HOH HOH . F 6 HOH A 40 1540 56 HOH HOH . G 6 HOH B 1 501 8 HOH HOH . G 6 HOH B 2 502 94 HOH HOH . G 6 HOH B 3 503 89 HOH HOH . G 6 HOH B 4 504 25 HOH HOH . G 6 HOH B 5 505 83 HOH HOH . G 6 HOH B 6 506 87 HOH HOH . G 6 HOH B 7 507 84 HOH HOH . G 6 HOH B 8 508 95 HOH HOH . G 6 HOH B 9 509 34 HOH HOH . G 6 HOH B 10 510 37 HOH HOH . G 6 HOH B 11 511 65 HOH HOH . G 6 HOH B 12 512 55 HOH HOH . G 6 HOH B 13 513 93 HOH HOH . G 6 HOH B 14 514 28 HOH HOH . G 6 HOH B 15 515 22 HOH HOH . G 6 HOH B 16 516 10 HOH HOH . G 6 HOH B 17 517 53 HOH HOH . G 6 HOH B 18 518 63 HOH HOH . G 6 HOH B 19 519 35 HOH HOH . G 6 HOH B 20 520 14 HOH HOH . G 6 HOH B 21 521 17 HOH HOH . G 6 HOH B 22 522 68 HOH HOH . G 6 HOH B 23 523 31 HOH HOH . G 6 HOH B 24 524 79 HOH HOH . G 6 HOH B 25 525 48 HOH HOH . G 6 HOH B 26 526 26 HOH HOH . G 6 HOH B 27 527 16 HOH HOH . G 6 HOH B 28 528 29 HOH HOH . G 6 HOH B 29 529 23 HOH HOH . G 6 HOH B 30 530 62 HOH HOH . G 6 HOH B 31 531 76 HOH HOH . G 6 HOH B 32 532 54 HOH HOH . G 6 HOH B 33 533 7 HOH HOH . G 6 HOH B 34 534 20 HOH HOH . G 6 HOH B 35 535 60 HOH HOH . G 6 HOH B 36 536 38 HOH HOH . G 6 HOH B 37 537 42 HOH HOH . G 6 HOH B 38 538 40 HOH HOH . G 6 HOH B 39 539 43 HOH HOH . G 6 HOH B 40 540 49 HOH HOH . G 6 HOH B 41 541 52 HOH HOH . G 6 HOH B 42 542 80 HOH HOH . G 6 HOH B 43 543 90 HOH HOH . G 6 HOH B 44 544 71 HOH HOH . G 6 HOH B 45 545 44 HOH HOH . G 6 HOH B 46 546 77 HOH HOH . G 6 HOH B 47 547 82 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 3 7.844 11.904 16.672 1 52.8 ? PB GDP 1401 A 1 HETATM 2 O O1B GDP . . . C 3 6.95 12.556 15.643 1 53.45 ? O1B GDP 1401 A 1 HETATM 3 O O2B GDP . . . C 3 7.059 11.711 17.947 1 45.6 ? O2B GDP 1401 A 1 HETATM 4 O O3B GDP . . . C 3 8.324 10.557 16.181 1 42.84 ? O3B GDP 1401 A 1 HETATM 5 O O3A GDP . . . C 3 9.147 12.8 16.944 1 42.6 ? O3A GDP 1401 A 1 HETATM 6 P PA GDP . . . C 3 9.259 14.379 16.649 1 39.6 ? PA GDP 1401 A 1 HETATM 7 O O1A GDP . . . C 3 9.356 14.705 15.184 1 52.09 ? O1A GDP 1401 A 1 HETATM 8 O O2A GDP . . . C 3 8.138 15.135 17.31 1 46.3 ? O2A GDP 1401 A 1 HETATM 9 O O5' GDP . . . C 3 10.673 14.705 17.326 1 56.26 ? O5' GDP 1401 A 1 HETATM 10 C C5' GDP . . . C 3 10.849 14.686 18.737 1 48.62 ? C5' GDP 1401 A 1 HETATM 11 C C4' GDP . . . C 3 12.201 15.312 19.025 1 46.75 ? C4' GDP 1401 A 1 HETATM 12 O O4' GDP . . . C 3 13.193 14.692 18.203 1 42.55 ? O4' GDP 1401 A 1 HETATM 13 C C3' GDP . . . C 3 12.204 16.787 18.665 1 52.15 ? C3' GDP 1401 A 1 HETATM 14 O O3' GDP . . . C 3 12.856 17.49 19.726 1 63.02 ? O3' GDP 1401 A 1 HETATM 15 C C2' GDP . . . C 3 13.056 16.876 17.423 1 46.65 ? C2' GDP 1401 A 1 HETATM 16 O O2' GDP . . . C 3 13.743 18.127 17.332 1 47.54 ? O2' GDP 1401 A 1 HETATM 17 C C1' GDP . . . C 3 14.003 15.704 17.608 1 44.67 ? C1' GDP 1401 A 1 HETATM 18 N N9 GDP . . . C 3 14.489 15.241 16.299 1 51.92 ? N9 GDP 1401 A 1 HETATM 19 C C8 GDP . . . C 3 13.782 15.249 15.151 1 46.73 ? C8 GDP 1401 A 1 HETATM 20 N N7 GDP . . . C 3 14.519 14.747 14.132 1 43.37 ? N7 GDP 1401 A 1 HETATM 21 C C5 GDP . . . C 3 15.718 14.396 14.632 1 45.62 ? C5 GDP 1401 A 1 HETATM 22 C C6 GDP . . . C 3 16.96 13.805 14.097 1 50.45 ? C6 GDP 1401 A 1 HETATM 23 O O6 GDP . . . C 3 17.06 13.501 12.889 1 57.2 ? O6 GDP 1401 A 1 HETATM 24 N N1 GDP . . . C 3 17.973 13.604 14.944 1 48.01 ? N1 GDP 1401 A 1 HETATM 25 C C2 GDP . . . C 3 17.898 13.917 16.249 1 45.18 ? C2 GDP 1401 A 1 HETATM 26 N N2 GDP . . . C 3 18.982 13.674 17.022 1 44.89 ? N2 GDP 1401 A 1 HETATM 27 N N3 GDP . . . C 3 16.792 14.463 16.816 1 42.35 ? N3 GDP 1401 A 1 HETATM 28 C C4 GDP . . . C 3 15.695 14.72 16.066 1 48.06 ? C4 GDP 1401 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #