data_7OH5 # _model_server_result.job_id eDXD-TRqN8-G4Sw70HcpEw _model_server_result.datetime_utc '2024-12-26 19:18:49' _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 7oh5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1504}' # _entry.id 7OH5 # _exptl.entry_id 7OH5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-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 7OH5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7OH5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 ? _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 7 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 BMA BMA C1 O1 . O3 HO3 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 B 1 NAG C 501 NAG 3 n C NAG 2 B 2 NAG C 502 NAG 3 n D NAG 1 D 1 NAG C 503 NAG 3 n D NAG 2 D 2 NAG C 504 NAG 4 n E NAG 1 E 1 NAG C 507 NAG 4 n E NAG 2 E 2 NAG C 508 NAG 4 n E BMA 3 E 3 BMA C 509 BMA 4 n E BMA 4 E 4 BMA C 510 BMA # 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 disulf ? disulf1 B SG CYS 80 C CYS 80 1_555 B SG CYS 123 C CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf2 B SG CYS 176 C CYS 176 1_555 B SG CYS 190 C CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? covale ? covale1 B ND2 ASN 199 C ASN 199 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 B ND2 ASN 216 C ASN 216 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 B ND2 ASN 237 C ASN 237 1_555 K C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 B ND2 ASN 288 C ASN 288 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 E O3 BMA . E BMA 3 1_555 E C1 BMA . E BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A OD2 ASP 560 A ASP 560 1_555 H MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc2 A O THR 562 A THR 562 1_555 H MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc3 A OD1 ASP 954 A ASP 954 1_555 H MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc4 F MG MG . A MG 1501 1_555 I O2A ADP . A ADP 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc5 H MG MG . A MG 1503 1_555 L O HOH . A HOH 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc6 H MG MG . A MG 1503 1_555 L O HOH . A HOH 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 150 n n PB O2B ADP sing 151 n n PB O3B ADP sing 152 n n PB O3A ADP sing 153 n n O2B HOB2 ADP sing 154 n n O3B HOB3 ADP sing 155 n n PA O1A ADP doub 156 n n PA O2A ADP sing 157 n n PA O3A ADP sing 158 n n PA O5' ADP sing 159 n n O2A HOA2 ADP sing 160 n n O5' C5' ADP sing 161 n n C5' C4' ADP sing 162 n n C5' "H5'1" ADP sing 163 n n C5' "H5'2" ADP sing 164 n n C4' O4' ADP sing 165 n n C4' C3' ADP sing 166 n n C4' H4' ADP sing 167 n n O4' C1' ADP sing 168 n n C3' O3' ADP sing 169 n n C3' C2' ADP sing 170 n n C3' H3' ADP sing 171 n n O3' HO3' ADP sing 172 n n C2' O2' ADP sing 173 n n C2' C1' ADP sing 174 n n C2' H2' ADP sing 175 n n O2' HO2' ADP sing 176 n n C1' N9 ADP sing 177 n n C1' H1' ADP sing 178 n n N9 C8 ADP sing 179 n y N9 C4 ADP sing 180 n y C8 N7 ADP doub 181 n y C8 H8 ADP sing 182 n n N7 C5 ADP sing 183 n y C5 C6 ADP sing 184 n y C5 C4 ADP doub 185 n y C6 N6 ADP sing 186 n n C6 N1 ADP doub 187 n y N6 HN61 ADP sing 188 n n N6 HN62 ADP sing 189 n n N1 C2 ADP sing 190 n y C2 N3 ADP doub 191 n y C2 H2 ADP sing 192 n n N3 C4 ADP sing 193 n y # _atom_sites.entry_id 7OH5 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 5 MG A 1 1501 2000 MG MG . G 6 ALF A 1 1502 2001 ALF ALF . H 5 MG A 1 1503 2002 MG MG . I 7 ADP A 1 1504 2003 ADP ADP . J 8 2Y5 A 1 1505 2101 2Y5 2Y5 . K 9 NAG C 1 501 505 NAG NAG . L 10 HOH A 1 1601 2005 HOH HOH . L 10 HOH A 2 1602 2004 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 ADP . . . I 7 126.879 143.588 184.663 1 74.13 ? PB ADP 1504 A 1 HETATM 2 O O1B ADP . . . I 7 126.71 143.072 183.276 1 74.13 ? O1B ADP 1504 A 1 HETATM 3 O O2B ADP . . . I 7 126.932 145.118 184.628 1 74.13 ? O2B ADP 1504 A 1 HETATM 4 O O3B ADP . . . I 7 128.154 143.065 185.243 1 74.13 ? O3B ADP 1504 A 1 HETATM 5 P PA ADP . . . I 7 125.487 141.711 186.457 1 74.13 ? PA ADP 1504 A 1 HETATM 6 O O1A ADP . . . I 7 125.068 140.584 185.534 1 74.13 ? O1A ADP 1504 A 1 HETATM 7 O O2A ADP . . . I 7 126.814 141.39 187.08 1 74.13 ? O2A ADP 1504 A 1 HETATM 8 O O3A ADP . . . I 7 125.59 143.114 185.623 1 74.13 ? O3A ADP 1504 A 1 HETATM 9 O O5' ADP . . . I 7 124.334 141.893 187.66 1 74.13 ? O5' ADP 1504 A 1 HETATM 10 C C5' ADP . . . I 7 124.692 141.572 189.02 1 74.13 ? C5' ADP 1504 A 1 HETATM 11 C C4' ADP . . . I 7 124.38 142.819 189.949 1 74.13 ? C4' ADP 1504 A 1 HETATM 12 O O4' ADP . . . I 7 124.518 142.39 191.444 1 74.13 ? O4' ADP 1504 A 1 HETATM 13 C C3' ADP . . . I 7 125.249 143.733 189.745 1 74.13 ? C3' ADP 1504 A 1 HETATM 14 O O3' ADP . . . I 7 124.639 144.875 189.069 1 74.13 ? O3' ADP 1504 A 1 HETATM 15 C C2' ADP . . . I 7 125.831 144.214 191.216 1 74.13 ? C2' ADP 1504 A 1 HETATM 16 O O2' ADP . . . I 7 125.066 145.343 191.716 1 74.13 ? O2' ADP 1504 A 1 HETATM 17 C C1' ADP . . . I 7 125.701 143.21 192.006 1 74.13 ? C1' ADP 1504 A 1 HETATM 18 N N9 ADP . . . I 7 126.952 142.392 192.005 1 74.13 ? N9 ADP 1504 A 1 HETATM 19 C C8 ADP . . . I 7 128.032 142.331 191.208 1 74.13 ? C8 ADP 1504 A 1 HETATM 20 N N7 ADP . . . I 7 128.842 141.372 191.743 1 74.13 ? N7 ADP 1504 A 1 HETATM 21 C C5 ADP . . . I 7 128.242 140.874 192.845 1 74.13 ? C5 ADP 1504 A 1 HETATM 22 C C6 ADP . . . I 7 128.612 139.903 193.749 1 74.13 ? C6 ADP 1504 A 1 HETATM 23 N N6 ADP . . . I 7 129.843 139.062 193.796 1 74.13 ? N6 ADP 1504 A 1 HETATM 24 N N1 ADP . . . I 7 127.793 139.59 194.799 1 74.13 ? N1 ADP 1504 A 1 HETATM 25 C C2 ADP . . . I 7 126.612 140.237 194.95 1 74.13 ? C2 ADP 1504 A 1 HETATM 26 N N3 ADP . . . I 7 126.239 141.205 194.052 1 74.13 ? N3 ADP 1504 A 1 HETATM 27 C C4 ADP . . . I 7 127.053 141.516 193.009 1 74.13 ? C4 ADP 1504 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #