data_7MO4 # _model_server_result.job_id hsp6UyYjUUPBzqNUYcnjqA _model_server_result.datetime_utc '2024-10-18 19:32:27' _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 7mo4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":301}' # _entry.id 7MO4 # _exptl.entry_id 7MO4 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 104.04 _cell.angle_gamma 90 _cell.entry_id 7MO4 _cell.length_a 67.66 _cell.length_b 61.24 _cell.length_c 69.75 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7MO4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,K 1 1 C,D,H,I,J,L 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 H N 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 A OG1 THR 25 A THR 24 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc2 E O2B GDP . A GDP 301 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc3 F MG MG . A MG 302 1_555 K O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc4 F MG MG . A MG 302 1_555 K O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc5 F MG MG . A MG 302 1_555 K O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc6 F MG MG . A MG 302 1_555 K O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc7 B SG CYS 20 B CYS 795 1_555 G ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc8 B SG CYS 23 B CYS 798 1_555 G ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc9 B SG CYS 34 B CYS 809 1_555 G ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc10 B SG CYS 37 B CYS 812 1_555 G ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc11 C OG1 THR 25 C THR 24 1_555 I MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc12 H O1B GDP . C GDP 301 1_555 I MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc13 I MG MG . C MG 302 1_555 L O HOH . C HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc14 I MG MG . C MG 302 1_555 L O HOH . C HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc15 I MG MG . C MG 302 1_555 L O HOH . C HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc16 I MG MG . C MG 302 1_555 L O HOH . C HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc17 D SG CYS 20 D CYS 795 1_555 J ZN ZN . D ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc18 D SG CYS 23 D CYS 798 1_555 J ZN ZN . D ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc19 D SG CYS 34 D CYS 809 1_555 J ZN ZN . D ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc20 D SG CYS 37 D CYS 812 1_555 J ZN ZN . D ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? # _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 7MO4 _atom_sites.fract_transf_matrix[1][1] 0.01478 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003696 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016329 _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] 0.014778 _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 E 3 GDP A 1 301 301 GDP GDP . F 4 MG A 1 302 401 MG MG . G 5 ZN B 1 901 901 ZN ZN . H 3 GDP C 1 301 301 GDP GDP . I 4 MG C 1 302 401 MG MG . J 5 ZN D 1 901 901 ZN ZN . K 6 HOH A 1 501 501 HOH HOH . K 6 HOH A 2 502 503 HOH HOH . K 6 HOH A 3 503 502 HOH HOH . K 6 HOH A 4 504 520 HOH HOH . K 6 HOH A 5 505 504 HOH HOH . K 6 HOH A 6 506 519 HOH HOH . K 6 HOH A 7 507 514 HOH HOH . K 6 HOH A 8 508 505 HOH HOH . K 6 HOH A 9 509 511 HOH HOH . K 6 HOH A 10 510 517 HOH HOH . K 6 HOH A 11 511 512 HOH HOH . K 6 HOH A 12 512 506 HOH HOH . K 6 HOH A 13 513 507 HOH HOH . K 6 HOH A 14 514 521 HOH HOH . K 6 HOH A 15 515 522 HOH HOH . K 6 HOH A 16 516 513 HOH HOH . K 6 HOH A 17 517 508 HOH HOH . K 6 HOH A 18 518 515 HOH HOH . L 6 HOH C 1 501 501 HOH HOH . L 6 HOH C 2 502 503 HOH HOH . L 6 HOH C 3 503 502 HOH HOH . L 6 HOH C 4 504 510 HOH HOH . L 6 HOH C 5 505 504 HOH HOH . L 6 HOH C 6 506 518 HOH HOH . L 6 HOH C 7 507 509 HOH HOH . L 6 HOH C 8 508 516 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 . . . H 3 27.603 5.96 2.742 1 95.41 ? PB GDP 301 C 1 HETATM 2 O O1B GDP . . . H 3 27.506 6.303 1.269 1 96.45 ? O1B GDP 301 C 1 HETATM 3 O O2B GDP . . . H 3 28.653 4.889 2.936 1 91.87 ? O2B GDP 301 C 1 HETATM 4 O O3B GDP . . . H 3 27.985 7.195 3.519 1 87.95 ? O3B GDP 301 C 1 HETATM 5 O O3A GDP . . . H 3 26.157 5.413 3.272 1 93.21 ? O3A GDP 301 C 1 HETATM 6 P PA GDP . . . H 3 25.165 4.473 2.355 1 89.35 ? PA GDP 301 C 1 HETATM 7 O O1A GDP . . . H 3 26 3.566 1.46 1 93.84 ? O1A GDP 301 C 1 HETATM 8 O O2A GDP . . . H 3 24.27 5.338 1.488 1 82.98 ? O2A GDP 301 C 1 HETATM 9 O O5' GDP . . . H 3 24.204 3.546 3.366 1 88.84 ? O5' GDP 301 C 1 HETATM 10 C C5' GDP . . . H 3 24.842 2.756 4.332 1 89.69 ? C5' GDP 301 C 1 HETATM 11 C C4' GDP . . . H 3 23.741 1.891 5.069 1 87.86 ? C4' GDP 301 C 1 HETATM 12 O O4' GDP . . . H 3 22.782 2.887 5.796 1 87.34 ? O4' GDP 301 C 1 HETATM 13 C C3' GDP . . . H 3 23.044 1.247 4.234 1 87.25 ? C3' GDP 301 C 1 HETATM 14 O O3' GDP . . . H 3 22.835 -0.142 4.713 1 85.94 ? O3' GDP 301 C 1 HETATM 15 C C2' GDP . . . H 3 21.575 2.027 4.119 1 86.71 ? C2' GDP 301 C 1 HETATM 16 O O2' GDP . . . H 3 20.521 1.082 3.791 1 85.51 ? O2' GDP 301 C 1 HETATM 17 C C1' GDP . . . H 3 21.379 2.486 5.292 1 86.85 ? C1' GDP 301 C 1 HETATM 18 N N9 GDP . . . H 3 20.452 3.671 5.404 1 86.86 ? N9 GDP 301 C 1 HETATM 19 C C8 GDP . . . H 3 21.012 4.706 4.72 1 86.74 ? C8 GDP 301 C 1 HETATM 20 N N7 GDP . . . H 3 20.187 5.765 4.826 1 86.36 ? N7 GDP 301 C 1 HETATM 21 C C5 GDP . . . H 3 19.144 5.399 5.578 1 86.66 ? C5 GDP 301 C 1 HETATM 22 C C6 GDP . . . H 3 17.892 6.151 6.054 1 86.76 ? C6 GDP 301 C 1 HETATM 23 O O6 GDP . . . H 3 17.726 7.296 5.746 1 87.09 ? O6 GDP 301 C 1 HETATM 24 N N1 GDP . . . H 3 16.926 5.48 6.867 1 87.9 ? N1 GDP 301 C 1 HETATM 25 C C2 GDP . . . H 3 17.136 4.102 7.235 1 87.16 ? C2 GDP 301 C 1 HETATM 26 N N2 GDP . . . H 3 16.164 3.386 8.068 1 86.39 ? N2 GDP 301 C 1 HETATM 27 N N3 GDP . . . H 3 18.335 3.391 6.778 1 86.6 ? N3 GDP 301 C 1 HETATM 28 C C4 GDP . . . H 3 19.323 4.095 5.938 1 86.64 ? C4 GDP 301 C 1 HETATM 29 H H5' GDP . . . H 3 25.296 3.324 4.973 1 109.52 ? H5' GDP 301 C 1 HETATM 30 H "H5''" GDP . . . H 3 25.487 2.171 3.904 1 109.52 ? "H5''" GDP 301 C 1 HETATM 31 H H4' GDP . . . H 3 24.125 1.254 5.692 1 107.33 ? H4' GDP 301 C 1 HETATM 32 H H3' GDP . . . H 3 23.487 1.26 3.372 1 106.59 ? H3' GDP 301 C 1 HETATM 33 H HO3' GDP . . . H 3 23.046 -0.687 4.096 1 105.02 ? HO3' GDP 301 C 1 HETATM 34 H H2' GDP . . . H 3 21.61 2.733 3.455 1 105.95 ? H2' GDP 301 C 1 HETATM 35 H HO2' GDP . . . H 3 20.868 0.365 3.496 1 104.51 ? HO2' GDP 301 C 1 HETATM 36 H H1' GDP . . . H 3 20.979 1.761 5.797 1 106.12 ? H1' GDP 301 C 1 HETATM 37 H H8 GDP . . . H 3 21.82 4.685 4.261 1 105.99 ? H8 GDP 301 C 1 HETATM 38 H HN1 GDP . . . H 3 16.223 5.896 7.135 1 107.37 ? HN1 GDP 301 C 1 HETATM 39 H HN21 GDP . . . H 3 15.458 3.785 8.347 1 105.56 ? HN21 GDP 301 C 1 HETATM 40 H HN22 GDP . . . H 3 16.307 2.565 8.278 1 105.56 ? HN22 GDP 301 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #