data_6Y4M # _model_server_result.job_id 8goNjgFwbE0XFqUhDiBZmg _model_server_result.datetime_utc '2024-10-19 06:37:17' _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 6y4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1001}' # _entry.id 6Y4M # _exptl.entry_id 6Y4M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 8 _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 90 _cell.angle_gamma 90 _cell.entry_id 6Y4M _cell.length_a 103.961 _cell.length_b 152.59 _cell.length_c 185.989 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y4M _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA _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 8 _struct_asym.id J _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 covale ? covale1 M C31 O9B . B O9B 1004 1_555 T N VAL . C VAL 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale2 N C5 O9H . B O9H 1005 1_555 O NBI OH5 . B OH5 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 N N3 O9H . B O9H 1005 1_555 T C VAL . C VAL 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc7 G O1G GTP . A GTP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc8 G O1B GTP . A GTP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc9 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc10 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc11 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc12 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc13 K MG MG . B MG 1002 1_555 Y O HOH . B HOH 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc14 K MG MG . B MG 1002 1_555 Z O HOH . C HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc15 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc16 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc17 C O THR 41 C THR 41 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc18 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc19 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc20 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc22 P O1G GTP . C GTP 1001 1_555 Q MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc23 P O1B GTP . C GTP 1001 1_555 Q MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc24 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc25 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc26 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc27 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc28 U O1G GTP . D GTP 1001 1_555 V MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc29 U O1B GTP . D GTP 1001 1_555 V MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc30 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc31 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc32 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc33 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? # _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 134 n n PB O2B GDP sing 135 n n PB O3B GDP sing 136 n n PB O3A GDP sing 137 n n O2B HOB2 GDP sing 138 n n O3B HOB3 GDP sing 139 n n O3A PA GDP sing 140 n n PA O1A GDP doub 141 n n PA O2A GDP sing 142 n n PA O5' GDP sing 143 n n O2A HOA2 GDP sing 144 n n O5' C5' GDP sing 145 n n C5' C4' GDP sing 146 n n C5' H5' GDP sing 147 n n C5' "H5''" GDP sing 148 n n C4' O4' GDP sing 149 n n C4' C3' GDP sing 150 n n C4' H4' GDP sing 151 n n O4' C1' GDP sing 152 n n C3' O3' GDP sing 153 n n C3' C2' GDP sing 154 n n C3' H3' GDP sing 155 n n O3' HO3' GDP sing 156 n n C2' O2' GDP sing 157 n n C2' C1' GDP sing 158 n n C2' H2' GDP sing 159 n n O2' HO2' GDP sing 160 n n C1' N9 GDP sing 161 n n C1' H1' GDP sing 162 n n N9 C8 GDP sing 163 n y N9 C4 GDP sing 164 n y C8 N7 GDP doub 165 n y C8 H8 GDP sing 166 n n N7 C5 GDP sing 167 n y C5 C6 GDP sing 168 n n C5 C4 GDP doub 169 n y C6 O6 GDP doub 170 n n C6 N1 GDP sing 171 n n N1 C2 GDP sing 172 n n N1 HN1 GDP sing 173 n n C2 N2 GDP sing 174 n n C2 N3 GDP doub 175 n n N2 HN21 GDP sing 176 n n N2 HN22 GDP sing 177 n n N3 C4 GDP sing 178 n n # _atom_sites.entry_id 6Y4M _atom_sites.fract_transf_matrix[1][1] 0.009619 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006554 _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] 0.005377 _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 G 5 GTP A 1 1001 1001 GTP GTP . H 6 MG A 1 1002 1002 MG MO6 . I 7 CA A 1 1003 1003 CA CA . J 8 GDP B 1 1001 1001 GDP GDP . K 6 MG B 1 1002 1002 MG MG . L 9 MES B 1 1003 1004 MES MES . M 10 O9B B 1 1004 2001 O9B ABB . N 11 O9H B 1 1005 2001 O9H ABB . O 12 OH5 B 1 1006 2001 OH5 ABB . P 5 GTP C 1 1001 1001 GTP GTP . Q 6 MG C 1 1002 1002 MG MO6 . R 7 CA C 1 1003 1003 CA CA . S 13 PGE C 1 1004 1004 PGE PGE . T 14 VAL C 1 1005 2001 VAL ABB . U 5 GTP D 1 1001 1001 GTP GTP . V 6 MG D 1 1002 1002 MG MO6 . W 15 ACP F 1 401 401 ACP ACP . X 16 HOH A 1 1101 1002 HOH MO6 . X 16 HOH A 2 1102 1002 HOH MO6 . X 16 HOH A 3 1103 1002 HOH MO6 . X 16 HOH A 4 1104 11 HOH HOH . X 16 HOH A 5 1105 1002 HOH MO6 . X 16 HOH A 6 1106 8 HOH HOH . X 16 HOH A 7 1107 10 HOH HOH . X 16 HOH A 8 1108 13 HOH HOH . X 16 HOH A 9 1109 7 HOH HOH . Y 16 HOH B 1 1101 20 HOH HOH . Y 16 HOH B 2 1102 18 HOH HOH . Y 16 HOH B 3 1103 5 HOH HOH . Y 16 HOH B 4 1104 16 HOH HOH . Y 16 HOH B 5 1105 4 HOH HOH . Y 16 HOH B 6 1106 14 HOH HOH . Y 16 HOH B 7 1107 6 HOH HOH . Y 16 HOH B 8 1108 21 HOH HOH . Y 16 HOH B 9 1109 1 HOH HOH . Y 16 HOH B 10 1110 9 HOH HOH . Y 16 HOH B 11 1111 19 HOH HOH . Z 16 HOH C 1 1101 1002 HOH MO6 . Z 16 HOH C 2 1102 1002 HOH MO6 . Z 16 HOH C 3 1103 1002 HOH MO6 . Z 16 HOH C 4 1104 15 HOH HOH . Z 16 HOH C 5 1105 1002 HOH MO6 . Z 16 HOH C 6 1106 2 HOH HOH . Z 16 HOH C 7 1107 3 HOH HOH . AA 16 HOH D 1 1101 1002 HOH MO6 . AA 16 HOH D 2 1102 17 HOH HOH . AA 16 HOH D 3 1103 1002 HOH MO6 . AA 16 HOH D 4 1104 1002 HOH MO6 . AA 16 HOH D 5 1105 1002 HOH MO6 . BA 16 HOH E 1 201 12 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 . . . J 8 -18.266 27.427 15.911 1 54.62 ? PB GDP 1001 B 1 HETATM 2 O O1B GDP . . . J 8 -17.525 26.41 15.071 1 55.69 ? O1B GDP 1001 B 1 HETATM 3 O O2B GDP . . . J 8 -18.899 26.907 17.183 1 52.4 ? O2B GDP 1001 B 1 HETATM 4 O O3B GDP . . . J 8 -19.163 28.319 15.079 1 55.09 ? O3B GDP 1001 B 1 HETATM 5 O O3A GDP . . . J 8 -17.111 28.404 16.471 1 52.85 ? O3A GDP 1001 B 1 HETATM 6 P PA GDP . . . J 8 -15.677 27.875 16.988 1 51.69 ? PA GDP 1001 B 1 HETATM 7 O O1A GDP . . . J 8 -14.685 28.196 15.895 1 53.78 ? O1A GDP 1001 B 1 HETATM 8 O O2A GDP . . . J 8 -15.819 26.462 17.497 1 51.37 ? O2A GDP 1001 B 1 HETATM 9 O O5' GDP . . . J 8 -15.393 28.807 18.266 1 50.22 ? O5' GDP 1001 B 1 HETATM 10 C C5' GDP . . . J 8 -14.483 29.905 18.256 1 50.42 ? C5' GDP 1001 B 1 HETATM 11 C C4' GDP . . . J 8 -13.817 30 19.623 1 50.17 ? C4' GDP 1001 B 1 HETATM 12 O O4' GDP . . . J 8 -13.415 28.698 20.037 1 50.45 ? O4' GDP 1001 B 1 HETATM 13 C C3' GDP . . . J 8 -12.545 30.828 19.597 1 51.15 ? C3' GDP 1001 B 1 HETATM 14 O O3' GDP . . . J 8 -12.315 31.401 20.893 1 50.27 ? O3' GDP 1001 B 1 HETATM 15 C C2' GDP . . . J 8 -11.478 29.819 19.246 1 52.26 ? C2' GDP 1001 B 1 HETATM 16 O O2' GDP . . . J 8 -10.178 30.216 19.692 1 54 ? O2' GDP 1001 B 1 HETATM 17 C C1' GDP . . . J 8 -11.988 28.583 19.964 1 51.53 ? C1' GDP 1001 B 1 HETATM 18 N N9 GDP . . . J 8 -11.621 27.327 19.273 1 51.46 ? N9 GDP 1001 B 1 HETATM 19 C C8 GDP . . . J 8 -11.971 26.95 18.029 1 52.24 ? C8 GDP 1001 B 1 HETATM 20 N N7 GDP . . . J 8 -11.462 25.724 17.74 1 52.8 ? N7 GDP 1001 B 1 HETATM 21 C C5 GDP . . . J 8 -10.784 25.312 18.822 1 52.41 ? C5 GDP 1001 B 1 HETATM 22 C C6 GDP . . . J 8 -10.007 24.116 19.199 1 53.63 ? C6 GDP 1001 B 1 HETATM 23 O O6 GDP . . . J 8 -9.868 23.174 18.387 1 54.77 ? O6 GDP 1001 B 1 HETATM 24 N N1 GDP . . . J 8 -9.463 24.084 20.429 1 53.04 ? N1 GDP 1001 B 1 HETATM 25 C C2 GDP . . . J 8 -9.6 25.095 21.31 1 51.28 ? C2 GDP 1001 B 1 HETATM 26 N N2 GDP . . . J 8 -9.019 24.989 22.527 1 51.76 ? N2 GDP 1001 B 1 HETATM 27 N N3 GDP . . . J 8 -10.298 26.219 21.031 1 49.94 ? N3 GDP 1001 B 1 HETATM 28 C C4 GDP . . . J 8 -10.894 26.371 19.829 1 51.03 ? C4 GDP 1001 B 1 # _model_server_stats.io_time_ms 121 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 207 _model_server_stats.query_time_ms 478 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #