data_5NM5 # _model_server_result.job_id YzicpmK88XeKXbFg5CrvQw _model_server_result.datetime_utc '2024-11-05 04:38:12' _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 5nm5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 5NM5 # _exptl.entry_id 5NM5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 97.32 _cell.angle_gamma 90 _cell.entry_id 5NM5 _cell.length_a 72.92 _cell.length_b 85.02 _cell.length_c 84.34 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NM5 _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 _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 6 _struct_asym.id F _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 O3G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc2 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc3 E MG MG . A MG 502 1_555 H O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc4 E MG MG . A MG 502 1_555 H O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc5 E MG MG . A MG 502 1_555 H O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc6 E MG MG . A MG 502 1_555 H O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _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 5NM5 _atom_sites.fract_transf_matrix[1][1] 0.013714 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001762 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011762 _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] 0.011954 _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 1 GTP GTP . E 5 MG A 1 502 503 MG MG . F 6 GDP B 1 501 1 GDP GDP . G 7 LOC B 1 502 1 LOC LOC . H 8 HOH A 1 601 38 HOH HOH . H 8 HOH A 2 602 7 HOH HOH . H 8 HOH A 3 603 8 HOH HOH . H 8 HOH A 4 604 13 HOH HOH . H 8 HOH A 5 605 41 HOH HOH . H 8 HOH A 6 606 25 HOH HOH . H 8 HOH A 7 607 18 HOH HOH . H 8 HOH A 8 608 10 HOH HOH . H 8 HOH A 9 609 12 HOH HOH . H 8 HOH A 10 610 29 HOH HOH . H 8 HOH A 11 611 11 HOH HOH . H 8 HOH A 12 612 26 HOH HOH . H 8 HOH A 13 613 33 HOH HOH . H 8 HOH A 14 614 48 HOH HOH . H 8 HOH A 15 615 30 HOH HOH . H 8 HOH A 16 616 3 HOH HOH . H 8 HOH A 17 617 32 HOH HOH . H 8 HOH A 18 618 30 HOH HOH . H 8 HOH A 19 619 10 HOH HOH . H 8 HOH A 20 620 7 HOH HOH . H 8 HOH A 21 621 39 HOH HOH . H 8 HOH A 22 622 41 HOH HOH . H 8 HOH A 23 623 27 HOH HOH . H 8 HOH A 24 624 33 HOH HOH . H 8 HOH A 25 625 4 HOH HOH . H 8 HOH A 26 626 28 HOH HOH . H 8 HOH A 27 627 20 HOH HOH . H 8 HOH A 28 628 40 HOH HOH . H 8 HOH A 29 629 43 HOH HOH . H 8 HOH A 30 630 47 HOH HOH . H 8 HOH A 31 631 50 HOH HOH . I 8 HOH B 1 601 37 HOH HOH . I 8 HOH B 2 602 22 HOH HOH . I 8 HOH B 3 603 36 HOH HOH . I 8 HOH B 4 604 2 HOH HOH . I 8 HOH B 5 605 12 HOH HOH . I 8 HOH B 6 606 6 HOH HOH . I 8 HOH B 7 607 11 HOH HOH . I 8 HOH B 8 608 53 HOH HOH . I 8 HOH B 9 609 16 HOH HOH . I 8 HOH B 10 610 38 HOH HOH . I 8 HOH B 11 611 8 HOH HOH . I 8 HOH B 12 612 1 HOH HOH . I 8 HOH B 13 613 23 HOH HOH . I 8 HOH B 14 614 14 HOH HOH . I 8 HOH B 15 615 37 HOH HOH . I 8 HOH B 16 616 22 HOH HOH . I 8 HOH B 17 617 26 HOH HOH . I 8 HOH B 18 618 46 HOH HOH . I 8 HOH B 19 619 49 HOH HOH . I 8 HOH B 20 620 15 HOH HOH . I 8 HOH B 21 621 18 HOH HOH . I 8 HOH B 22 622 45 HOH HOH . I 8 HOH B 23 623 2 HOH HOH . I 8 HOH B 24 624 52 HOH HOH . I 8 HOH B 25 625 44 HOH HOH . I 8 HOH B 26 626 32 HOH HOH . I 8 HOH B 27 627 5 HOH HOH . J 8 HOH F 1 201 35 HOH HOH . J 8 HOH F 2 202 21 HOH HOH . J 8 HOH F 3 203 23 HOH HOH . J 8 HOH F 4 204 24 HOH HOH . J 8 HOH F 5 205 36 HOH HOH . J 8 HOH F 6 206 51 HOH HOH . J 8 HOH F 7 207 9 HOH HOH . J 8 HOH F 8 208 13 HOH HOH . J 8 HOH F 9 209 3 HOH HOH . J 8 HOH F 10 210 35 HOH HOH . J 8 HOH F 11 211 17 HOH HOH . J 8 HOH F 12 212 42 HOH HOH . J 8 HOH F 13 213 34 HOH HOH . J 8 HOH F 14 214 19 HOH HOH . J 8 HOH F 15 215 29 HOH HOH . J 8 HOH F 16 216 31 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 . . . F 6 75.578 11.714 53.529 1 70.08 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . F 6 76.294 12.599 52.465 1 72.33 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . F 6 76.192 10.497 53.827 1 65.73 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . F 6 75.421 12.653 54.678 1 76.84 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . F 6 74.172 11.397 52.884 1 61.76 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . F 6 73.958 10.44 51.642 1 65.1 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . F 6 75.298 10.344 51.016 1 67.71 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . F 6 73.484 9.073 52.09 1 70.79 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . F 6 72.895 11.042 50.632 1 61.2 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . F 6 71.555 10.596 50.456 1 64.32 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . F 6 71.221 10.845 49.016 1 63.54 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . F 6 72.228 10.176 48.237 1 65.26 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . F 6 69.889 10.279 48.528 1 62.14 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . F 6 69.389 10.977 47.392 1 62.36 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . F 6 70.276 8.865 48.121 1 64.11 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . F 6 69.474 8.331 47.076 1 70.72 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . F 6 71.644 9.114 47.517 1 63.65 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . F 6 72.52 7.966 47.62 1 66.55 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . F 6 73.137 7.503 48.746 1 63.94 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . F 6 73.948 6.504 48.522 1 61.59 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . F 6 73.869 6.306 47.151 1 66.66 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . F 6 74.608 5.431 46.269 1 66.35 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . F 6 75.452 4.597 46.592 1 63.02 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . F 6 74.296 5.643 44.938 1 64.73 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . F 6 73.381 6.55 44.472 1 67.93 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . F 6 73.108 6.512 43.164 1 67.96 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . F 6 72.692 7.372 45.268 1 67.98 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . F 6 72.984 7.199 46.584 1 68.9 ? C4 GDP 501 B 1 HETATM 29 H H5' GDP . . . F 6 70.882 11.107 51.144 1 66.09 ? H5' GDP 501 B 1 HETATM 30 H "H5''" GDP . . . F 6 71.566 9.534 50.694 1 64.24 ? "H5''" GDP 501 B 1 HETATM 31 H H4' GDP . . . F 6 71.337 11.9 48.773 1 64.15 ? H4' GDP 501 B 1 HETATM 32 H H3' GDP . . . F 6 69.136 10.274 49.313 1 62.54 ? H3' GDP 501 B 1 HETATM 33 H HO3' GDP . . . F 6 68.64 10.455 46.999 1 61.82 ? HO3' GDP 501 B 1 HETATM 34 H H2' GDP . . . F 6 70.339 8.205 48.984 1 64.36 ? H2' GDP 501 B 1 HETATM 35 H HO2' GDP . . . F 6 68.573 8.185 47.462 1 70.96 ? HO2' GDP 501 B 1 HETATM 36 H H1' GDP . . . F 6 71.582 9.439 46.48 1 63.87 ? H1' GDP 501 B 1 HETATM 37 H H8 GDP . . . F 6 73.012 7.962 49.726 1 64.47 ? H8 GDP 501 B 1 HETATM 38 H HN1 GDP . . . F 6 74.817 5.077 44.278 1 64.74 ? HN1 GDP 501 B 1 HETATM 39 H HN21 GDP . . . F 6 72.443 7.157 42.754 1 67.72 ? HN21 GDP 501 B 1 HETATM 40 H HN22 GDP . . . F 6 73.525 5.842 42.525 1 68.05 ? HN22 GDP 501 B 1 # _model_server_stats.io_time_ms 37 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 40 #