data_6CAB # _model_server_result.job_id ApQfvxpFc9T4LwjTjELaYA _model_server_result.datetime_utc '2024-11-21 23:23:30' _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 6cab # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":102}' # _entry.id 6CAB # _exptl.entry_id 6CAB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 6CAB _cell.length_a 48.707 _cell.length_b 48.707 _cell.length_c 80.58 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6CAB _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 3 2 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,H,I,J,K,L _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 ? 2 C N N ? 2 D N N ? 2 G N N ? 2 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 A O3' LCC 1 A LCC 1 1_555 A P LCC 2 A LCC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.585 ? covale ? covale2 A O3' LCC 2 A LCC 2 1_555 A P LCC 3 A LCC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.642 ? covale ? covale3 A O3' LCC 3 A LCC 3 1_555 A P LCG 4 A LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.629 ? covale ? covale4 A O3' LCG 4 A LCG 4 1_555 A P A 5 A A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.64 ? covale ? covale5 B O3' LCC 1 B LCC 1 1_555 B P LCC 2 B LCC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.622 ? covale ? covale6 B O3' LCC 2 B LCC 2 1_555 B P LCC 3 B LCC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.67 ? covale ? covale7 B O3' LCC 3 B LCC 3 1_555 B P LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.673 ? covale ? covale8 B O3' LCG 4 B LCG 4 1_555 B P A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.676 ? metalc ? metalc1 A O6 G 14 A G 14 1_555 E SR SR . A SR 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc2 C N7 5GP . A 5GP 101 1_555 E SR SR . A SR 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc3 C O6 5GP . A 5GP 101 1_555 E SR SR . A SR 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc4 C O3' 5GP . A 5GP 101 1_555 F SR SR . A SR 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc5 C O3' 5GP . A 5GP 101 1_555 F SR SR . A SR 104 2_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc6 E SR SR . A SR 103 1_555 L O HOH . B HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.81 ? metalc ? metalc7 K O HOH . A HOH 202 1_555 I SR SR . B SR 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc8 B O6 G 14 B G 14 1_555 I SR SR . B SR 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc9 H O6 5GP . B 5GP 102 1_555 I SR SR . B SR 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? metalc ? metalc10 H O3' 5GP . B 5GP 102 1_555 J SR SR . B SR 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc11 H O3' 5GP . B 5GP 102 1_555 J SR SR . B SR 104 2_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? hydrog WATSON-CRICK hydrog1 A N1 LCG 4 A LCG 4 1_555 B N3 C 13 B C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 LCG 4 A LCG 4 1_555 B O2 C 13 B C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 LCG 4 A LCG 4 1_555 B N4 C 13 B C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 A 5 A A 5 1_555 B N3 U 12 B U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 A 5 A A 5 1_555 B O4 U 12 B U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 C 6 A C 6 1_555 B N1 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N4 C 6 A C 6 1_555 B O6 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O2 C 6 A C 6 1_555 B N2 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 U 7 A U 7 1_555 B N1 A 10 B A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O4 U 7 A U 7 1_555 B N6 A 10 B A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 U 8 A U 8 1_555 B N1 A 9 B A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O4 U 8 A U 8 1_555 B N6 A 9 B A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 A 9 A A 9 1_555 B N3 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 A 9 A A 9 1_555 B O4 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 A 10 A A 10 1_555 B N3 U 7 B U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 A 10 A A 10 1_555 B O4 U 7 B U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 G 11 A G 11 1_555 B N3 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N2 G 11 A G 11 1_555 B O2 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O6 G 11 A G 11 1_555 B N4 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N3 U 12 A U 12 1_555 B N1 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O4 U 12 A U 12 1_555 B N6 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 C 13 A C 13 1_555 B N1 LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N4 C 13 A C 13 1_555 B O6 LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O2 C 13 A C 13 1_555 B N2 LCG 4 B LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 6CAB _atom_sites.fract_transf_matrix[1][1] 0.020531 _atom_sites.fract_transf_matrix[1][2] 0.011854 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023707 _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] 0.01241 _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 5GP A 1 101 101 5GP G . D 2 5GP A 1 102 102 5GP G . E 3 SR A 1 103 103 SR SR . F 3 SR A 1 104 105 SR SR . G 2 5GP B 1 101 101 5GP G . H 2 5GP B 1 102 102 5GP G . I 3 SR B 1 103 103 SR SR . J 3 SR B 1 104 106 SR SR . K 4 HOH A 1 201 201 HOH HOH . K 4 HOH A 2 202 202 HOH HOH . K 4 HOH A 3 203 203 HOH HOH . L 4 HOH B 1 201 201 HOH HOH . L 4 HOH B 2 202 202 HOH HOH . L 4 HOH B 3 203 203 HOH HOH . L 4 HOH B 4 204 204 HOH HOH . L 4 HOH B 5 205 205 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 . . . D 2 29.852 -10.346 76.757 1 172.76 ? P 5GP 102 A 1 HETATM 2 O O1P 5GP . . . D 2 30.007 -11.721 77.279 1 166.18 ? O1P 5GP 102 A 1 HETATM 3 O O2P 5GP . . . D 2 29.402 -10.218 75.361 1 159.96 ? O2P 5GP 102 A 1 HETATM 4 O O3P 5GP . . . D 2 31.029 -9.38 77.153 1 159.52 ? O3P 5GP 102 A 1 HETATM 5 O O5' 5GP . . . D 2 28.587 -9.691 77.538 1 151.03 ? O5' 5GP 102 A 1 HETATM 6 C C5' 5GP . . . D 2 27.622 -10.467 78.286 1 119.33 ? C5' 5GP 102 A 1 HETATM 7 C C4' 5GP . . . D 2 26.456 -9.586 78.791 1 104 ? C4' 5GP 102 A 1 HETATM 8 O O4' 5GP . . . D 2 26.72 -9.34 80.19 1 92.3 ? O4' 5GP 102 A 1 HETATM 9 C C3' 5GP . . . D 2 26.26 -8.187 78.142 1 96.79 ? C3' 5GP 102 A 1 HETATM 10 O O3' 5GP . . . D 2 25.013 -8.128 77.458 1 106.95 ? O3' 5GP 102 A 1 HETATM 11 C C2' 5GP . . . D 2 26.203 -7.228 79.29 1 92.77 ? C2' 5GP 102 A 1 HETATM 12 O O2' 5GP . . . D 2 24.829 -7.02 79.72 1 91.36 ? O2' 5GP 102 A 1 HETATM 13 C C1' 5GP . . . D 2 27.014 -7.943 80.39 1 81.74 ? C1' 5GP 102 A 1 HETATM 14 N N9 5GP . . . D 2 28.465 -7.553 80.427 1 73.81 ? N9 5GP 102 A 1 HETATM 15 C C8 5GP . . . D 2 29.666 -8.179 80.205 1 76.95 ? C8 5GP 102 A 1 HETATM 16 N N7 5GP . . . D 2 30.694 -7.396 80.388 1 71.63 ? N7 5GP 102 A 1 HETATM 17 C C5 5GP . . . D 2 30.136 -6.181 80.753 1 69.4 ? C5 5GP 102 A 1 HETATM 18 C C6 5GP . . . D 2 30.758 -4.941 81.073 1 64.49 ? C6 5GP 102 A 1 HETATM 19 O O6 5GP . . . D 2 31.961 -4.671 81.1 1 64.02 ? O6 5GP 102 A 1 HETATM 20 N N1 5GP . . . D 2 29.823 -3.959 81.38 1 63.14 ? N1 5GP 102 A 1 HETATM 21 C C2 5GP . . . D 2 28.463 -4.149 81.381 1 57.96 ? C2 5GP 102 A 1 HETATM 22 N N2 5GP . . . D 2 27.723 -3.084 81.694 1 56.53 ? N2 5GP 102 A 1 HETATM 23 N N3 5GP . . . D 2 27.871 -5.294 81.075 1 61.77 ? N3 5GP 102 A 1 HETATM 24 C C4 5GP . . . D 2 28.762 -6.261 80.774 1 72.62 ? C4 5GP 102 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 24 #