data_7BUM # _model_server_result.job_id xnV0R08LYUU_STB4OHM_Eg _model_server_result.datetime_utc '2024-11-08 09:34:23' _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 7bum # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":603}' # _entry.id 7BUM # _exptl.entry_id 7BUM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-MONOPHOSPHATE" _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 93.93 _cell.angle_gamma 90 _cell.entry_id 7BUM _cell.length_a 48.337 _cell.length_b 109.592 _cell.length_c 75.87 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BUM _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 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 covale ? covale1 D P AMP . A AMP 602 1_555 E O2' 5GP . A 5GP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.558 ? covale ? covale2 G P AMP . B AMP 602 1_555 H O2' 5GP . B 5GP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.562 ? metalc ? metalc1 A NE2 HIS 378 A HIS 378 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc2 A SG CYS 384 A CYS 384 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc3 A SG CYS 385 A CYS 385 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc4 A SG CYS 392 A CYS 392 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc5 B NE2 HIS 378 B HIS 378 1_555 F ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc6 B SG CYS 384 B CYS 384 1_555 F ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc7 B SG CYS 385 B CYS 385 1_555 F ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc8 B SG CYS 392 B CYS 392 1_555 F ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 5GP _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _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 P O1P 5GP doub 1 n n P O2P 5GP sing 2 n n P O3P 5GP sing 3 n n P O5' 5GP sing 4 n n O2P HOP2 5GP sing 5 n n O3P HOP3 5GP sing 6 n n O5' C5' 5GP sing 7 n n C5' C4' 5GP sing 8 n n C5' "H5'1" 5GP sing 9 n n C5' "H5'2" 5GP sing 10 n n C4' O4' 5GP sing 11 n n C4' C3' 5GP sing 12 n n C4' H4' 5GP sing 13 n n O4' C1' 5GP sing 14 n n C3' O3' 5GP sing 15 n n C3' C2' 5GP sing 16 n n C3' H3' 5GP sing 17 n n O3' HO3' 5GP sing 18 n n C2' O2' 5GP sing 19 n n C2' C1' 5GP sing 20 n n C2' H2' 5GP sing 21 n n O2' HO2' 5GP sing 22 n n C1' N9 5GP sing 23 n n C1' H1' 5GP sing 24 n n N9 C8 5GP sing 25 n y N9 C4 5GP sing 26 n y C8 N7 5GP doub 27 n y C8 H8 5GP sing 28 n n N7 C5 5GP sing 29 n y C5 C6 5GP sing 30 n n C5 C4 5GP doub 31 n y C6 O6 5GP doub 32 n n C6 N1 5GP sing 33 n n N1 C2 5GP sing 34 n n N1 HN1 5GP sing 35 n n C2 N2 5GP sing 36 n n C2 N3 5GP doub 37 n n N2 HN21 5GP sing 38 n n N2 HN22 5GP sing 39 n n N3 C4 5GP sing 40 n n # _atom_sites.entry_id 7BUM _atom_sites.fract_transf_matrix[1][1] 0.020688 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001422 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009125 _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] 0.013212 _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 2 ZN A 1 601 601 ZN ZN . D 3 AMP A 1 602 701 AMP LIG . E 4 5GP A 1 603 801 5GP GMP . F 2 ZN B 1 601 601 ZN ZN . G 3 AMP B 1 602 701 AMP LIG . H 4 5GP B 1 603 801 5GP GMP . I 5 HOH A 1 701 31 HOH HOH . I 5 HOH A 2 702 23 HOH HOH . I 5 HOH A 3 703 17 HOH HOH . I 5 HOH A 4 704 6 HOH HOH . I 5 HOH A 5 705 36 HOH HOH . I 5 HOH A 6 706 16 HOH HOH . I 5 HOH A 7 707 33 HOH HOH . I 5 HOH A 8 708 2 HOH HOH . I 5 HOH A 9 709 15 HOH HOH . I 5 HOH A 10 710 1 HOH HOH . I 5 HOH A 11 711 27 HOH HOH . I 5 HOH A 12 712 12 HOH HOH . I 5 HOH A 13 713 26 HOH HOH . I 5 HOH A 14 714 41 HOH HOH . I 5 HOH A 15 715 4 HOH HOH . I 5 HOH A 16 716 3 HOH HOH . I 5 HOH A 17 717 24 HOH HOH . I 5 HOH A 18 718 43 HOH HOH . I 5 HOH A 19 719 34 HOH HOH . I 5 HOH A 20 720 13 HOH HOH . I 5 HOH A 21 721 11 HOH HOH . J 5 HOH B 1 701 7 HOH HOH . J 5 HOH B 2 702 22 HOH HOH . J 5 HOH B 3 703 20 HOH HOH . J 5 HOH B 4 704 21 HOH HOH . J 5 HOH B 5 705 38 HOH HOH . J 5 HOH B 6 706 9 HOH HOH . J 5 HOH B 7 707 10 HOH HOH . J 5 HOH B 8 708 39 HOH HOH . J 5 HOH B 9 709 8 HOH HOH . J 5 HOH B 10 710 18 HOH HOH . J 5 HOH B 11 711 30 HOH HOH . J 5 HOH B 12 712 32 HOH HOH . J 5 HOH B 13 713 25 HOH HOH . J 5 HOH B 14 714 19 HOH HOH . J 5 HOH B 15 715 37 HOH HOH . J 5 HOH B 16 716 5 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 P 5GP . . . H 4 17.093 -14.525 8.668 1 73.53 ? P 5GP 603 B 1 HETATM 2 O O1P 5GP . . . H 4 18.069 -14.569 7.511 1 69.99 ? O1P 5GP 603 B 1 HETATM 3 O O2P 5GP . . . H 4 17.674 -13.774 9.847 1 74.14 ? O2P 5GP 603 B 1 HETATM 4 O O3P 5GP . . . H 4 16.787 -15.929 9.135 1 75.7 ? O3P 5GP 603 B 1 HETATM 5 O O5' 5GP . . . H 4 15.702 -13.801 8.137 1 70.86 ? O5' 5GP 603 B 1 HETATM 6 C C5' 5GP . . . H 4 15.485 -12.457 8.455 1 68.9 ? C5' 5GP 603 B 1 HETATM 7 C C4' 5GP . . . H 4 14.381 -11.817 7.613 1 68.81 ? C4' 5GP 603 B 1 HETATM 8 O O4' 5GP . . . H 4 14.991 -10.538 6.819 1 66.68 ? O4' 5GP 603 B 1 HETATM 9 C C3' 5GP . . . H 4 13.84 -12.592 6.714 1 71.1 ? C3' 5GP 603 B 1 HETATM 10 O O3' 5GP . . . H 4 12.39 -12.209 6.565 1 70.71 ? O3' 5GP 603 B 1 HETATM 11 C C2' 5GP . . . H 4 14.541 -12.254 5.403 1 71.92 ? C2' 5GP 603 B 1 HETATM 12 O O2' 5GP . . . H 4 13.752 -12.581 4.318 1 69.86 ? O2' 5GP 603 B 1 HETATM 13 C C1' 5GP . . . H 4 14.85 -10.729 5.553 1 68.15 ? C1' 5GP 603 B 1 HETATM 14 N N9 5GP . . . H 4 16.108 -10.311 4.843 1 67.25 ? N9 5GP 603 B 1 HETATM 15 C C8 5GP . . . H 4 17.37 -10.748 5.073 1 65.33 ? C8 5GP 603 B 1 HETATM 16 N N7 5GP . . . H 4 18.198 -10.103 4.216 1 62.67 ? N7 5GP 603 B 1 HETATM 17 C C5 5GP . . . H 4 17.472 -9.27 3.455 1 63.35 ? C5 5GP 603 B 1 HETATM 18 C C6 5GP . . . H 4 17.831 -8.285 2.304 1 61.91 ? C6 5GP 603 B 1 HETATM 19 O O6 5GP . . . H 4 18.944 -8.118 1.901 1 62.21 ? O6 5GP 603 B 1 HETATM 20 N N1 5GP . . . H 4 16.776 -7.543 1.69 1 60.5 ? N1 5GP 603 B 1 HETATM 21 C C2 5GP . . . H 4 15.413 -7.697 2.13 1 58.57 ? C2 5GP 603 B 1 HETATM 22 N N2 5GP . . . H 4 14.363 -6.933 1.491 1 59.65 ? N2 5GP 603 B 1 HETATM 23 N N3 5GP . . . H 4 15.091 -8.613 3.213 1 59.81 ? N3 5GP 603 B 1 HETATM 24 C C4 5GP . . . H 4 16.169 -9.41 3.859 1 63.97 ? C4 5GP 603 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 24 #