data_2Y3I # _model_server_result.job_id 6oObIWmKoMMDrTB92w-rhw _model_server_result.datetime_utc '2024-12-26 15:07:29' _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 2y3i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1418}' # _entry.id 2Y3I # _exptl.entry_id 2Y3I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "L-ADENOSINE-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 90 _cell.angle_gamma 90 _cell.entry_id 2Y3I _cell.length_a 38.419 _cell.length_b 103.877 _cell.length_c 203.094 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Y3I _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,E,F,G,M 1 1 B,H,I,J,K,L,N 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 ? 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 metalc ? metalc1 A OD1 ASP 375 A ASP 374 1_555 C MG MG . A MG 1416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc2 C MG MG . A MG 1416 1_555 E O3B LA8 . A LA8 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc3 B OD1 ASP 375 D ASP 374 1_555 J MG MG . D MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc4 H O1A LA8 . D LA8 1416 1_555 J MG MG . D MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc5 H O3B LA8 . D LA8 1416 1_555 J MG MG . D MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id LA8 _chem_comp.mon_nstd_flag . _chem_comp.name "L-ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms L-ADP # 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 C2 N1 LA8 doub 194 n y N1 C6 LA8 sing 195 n y C2 N3 LA8 sing 196 n y C2 H2 LA8 sing 197 n n N3 C4 LA8 doub 198 n y C4 N9 LA8 sing 199 n y C4 C5 LA8 sing 200 n y C6 C5 LA8 doub 201 n y C5 N7 LA8 sing 202 n y C6 N6 LA8 sing 203 n n N6 HN6 LA8 sing 204 n n N6 HN6A LA8 sing 205 n n C8 N7 LA8 doub 206 n y N9 C8 LA8 sing 207 n y C8 H8 LA8 sing 208 n n C1' N9 LA8 sing 209 n n O1A PA LA8 doub 210 n n PA O5' LA8 sing 211 n n PA O3A LA8 sing 212 n n PA O2A LA8 sing 213 n n O2B PB LA8 doub 214 n n O1B PB LA8 sing 215 n n PB O3A LA8 sing 216 n n PB O3B LA8 sing 217 n n C3' C1' LA8 sing 218 n n O4' C1' LA8 sing 219 n n C1' H1' LA8 sing 220 n n O1B HO1B LA8 sing 221 n n O2' C2' LA8 sing 222 n n C2' C4' LA8 sing 223 n n C2' C3' LA8 sing 224 n n C2' H2' LA8 sing 225 n n O2' HO2' LA8 sing 226 n n O2A HO2A LA8 sing 227 n n C3' O3' LA8 sing 228 n n C3' H3' LA8 sing 229 n n O3' HO3' LA8 sing 230 n n O3B HO3B LA8 sing 231 n n C5' C4' LA8 sing 232 n n C4' O4' LA8 sing 233 n n C4' H4' LA8 sing 234 n n C5' O5' LA8 sing 235 n n C5' H5' LA8 sing 236 n n C5' "H5'A" LA8 sing 237 n n # _atom_sites.entry_id 2Y3I _atom_sites.fract_transf_matrix[1][1] 0.026029 _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] 0.009627 _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] 0.004924 _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 MG A 1 1416 1416 MG MG . D 3 CL A 1 1417 1417 CL CL . E 4 LA8 A 1 1418 1418 LA8 LA8 . F 5 ALF A 1 1419 1419 ALF ALF . G 6 3PG A 1 1420 1420 3PG 3PG . H 4 LA8 D 1 1416 1416 LA8 LA8 . I 5 ALF D 1 1417 1417 ALF ALF . J 2 MG D 1 1418 1418 MG MG . K 3 CL D 1 1419 1419 CL CL . L 6 3PG D 1 1420 1420 3PG 3PG . M 7 HOH A 1 2001 2001 HOH HOH . M 7 HOH A 2 2002 2002 HOH HOH . M 7 HOH A 3 2003 2003 HOH HOH . M 7 HOH A 4 2004 2004 HOH HOH . M 7 HOH A 5 2005 2005 HOH HOH . M 7 HOH A 6 2006 2006 HOH HOH . M 7 HOH A 7 2007 2007 HOH HOH . M 7 HOH A 8 2008 2008 HOH HOH . N 7 HOH D 1 2001 2001 HOH HOH . N 7 HOH D 2 2002 2002 HOH HOH . N 7 HOH D 3 2003 2003 HOH HOH . N 7 HOH D 4 2004 2004 HOH HOH . N 7 HOH D 5 2005 2005 HOH HOH . N 7 HOH D 6 2006 2006 HOH HOH . N 7 HOH D 7 2007 2007 HOH HOH . N 7 HOH D 8 2008 2008 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 N N1 LA8 . . . E 4 -18.132 -16.04 -12.367 1 28.14 ? N1 LA8 1418 A 1 HETATM 2 C C2 LA8 . . . E 4 -17.551 -15.075 -11.658 1 27.95 ? C2 LA8 1418 A 1 HETATM 3 N N3 LA8 . . . E 4 -17.083 -13.974 -12.229 1 27.79 ? N3 LA8 1418 A 1 HETATM 4 C C4 LA8 . . . E 4 -17.176 -13.795 -13.554 1 27.37 ? C4 LA8 1418 A 1 HETATM 5 C C5 LA8 . . . E 4 -17.771 -14.777 -14.313 1 27.75 ? C5 LA8 1418 A 1 HETATM 6 C C6 LA8 . . . E 4 -18.259 -15.918 -13.696 1 28.2 ? C6 LA8 1418 A 1 HETATM 7 N N6 LA8 . . . E 4 -18.839 -16.874 -14.418 1 28.93 ? N6 LA8 1418 A 1 HETATM 8 N N7 LA8 . . . E 4 -17.746 -14.383 -15.57 1 28.3 ? N7 LA8 1418 A 1 HETATM 9 C C8 LA8 . . . E 4 -17.156 -13.195 -15.614 1 27.87 ? C8 LA8 1418 A 1 HETATM 10 N N9 LA8 . . . E 4 -16.802 -12.831 -14.389 1 27.55 ? N9 LA8 1418 A 1 HETATM 11 P PA LA8 . . . E 4 -20.002 -7.278 -12.697 1 26.57 ? PA LA8 1418 A 1 HETATM 12 P PB LA8 . . . E 4 -19.781 -4.686 -13.507 1 27.1 ? PB LA8 1418 A 1 HETATM 13 C C1' LA8 . . . E 4 -16.112 -11.536 -14.085 1 27.67 ? C1' LA8 1418 A 1 HETATM 14 O O1A LA8 . . . E 4 -20.344 -6.493 -11.325 1 27 ? O1A LA8 1418 A 1 HETATM 15 O O1B LA8 . . . E 4 -21.381 -4.541 -13.685 1 27.74 ? O1B LA8 1418 A 1 HETATM 16 C C2' LA8 . . . E 4 -16.376 -10.579 -11.909 1 27.18 ? C2' LA8 1418 A 1 HETATM 17 O O2' LA8 . . . E 4 -15.572 -9.698 -11.153 1 27.72 ? O2' LA8 1418 A 1 HETATM 18 O O2A LA8 . . . E 4 -21.134 -8.033 -13.259 1 26.66 ? O2A LA8 1418 A 1 HETATM 19 O O2B LA8 . . . E 4 -19.117 -3.921 -14.731 1 25.86 ? O2B LA8 1418 A 1 HETATM 20 C C3' LA8 . . . E 4 -15.421 -11.39 -12.729 1 27.12 ? C3' LA8 1418 A 1 HETATM 21 O O3' LA8 . . . E 4 -14.273 -10.589 -12.909 1 26.73 ? O3' LA8 1418 A 1 HETATM 22 O O3A LA8 . . . E 4 -19.493 -6.2 -13.733 1 27.04 ? O3A LA8 1418 A 1 HETATM 23 O O3B LA8 . . . E 4 -19.32 -4.148 -12.212 1 27.1 ? O3B LA8 1418 A 1 HETATM 24 C C4' LA8 . . . E 4 -17.085 -9.755 -12.965 1 27.66 ? C4' LA8 1418 A 1 HETATM 25 O O4' LA8 . . . E 4 -17.187 -10.597 -14.096 1 28.21 ? O4' LA8 1418 A 1 HETATM 26 C C5' LA8 . . . E 4 -18.55 -9.468 -12.639 1 28.05 ? C5' LA8 1418 A 1 HETATM 27 O O5' LA8 . . . E 4 -18.714 -8.095 -12.335 1 28.05 ? O5' LA8 1418 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #