data_4RIW # _model_server_result.job_id 9dBDHhX0mXk5S9ykM6AiKw _model_server_result.datetime_utc '2024-12-04 12:47:55' _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 4riw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1001}' # _entry.id 4RIW # _exptl.entry_id 4RIW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "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 110.89 _cell.angle_gamma 90 _cell.entry_id 4RIW _cell.length_a 65.78 _cell.length_b 154.64 _cell.length_c 86.97 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RIW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,E,F,G,H 1 1 C,D,I,J,K,L 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 ? 5 G N N ? 5 K 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 ASN 145 A ASN 820 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc2 A OD2 ASP 158 A ASP 833 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc3 E O3A ANP . A ANP 1101 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc4 B OD1 ASN 165 B ASN 818 1_555 H MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc5 B OD2 ASP 178 B ASP 831 1_555 H MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc6 G O1B ADP . B ADP 1001 1_555 H MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc7 G O2A ADP . B ADP 1001 1_555 H MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc8 C OD1 ASN 145 C ASN 820 1_555 J MG MG . C MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc9 C OD2 ASP 158 C ASP 833 1_555 J MG MG . C MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc10 I O3A ANP . C ANP 1101 1_555 J MG MG . C MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc11 I O2A ANP . C ANP 1101 1_555 J MG MG . C MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc12 D OD1 ASN 165 D ASN 818 1_555 L MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc13 D OD2 ASP 178 D ASP 831 1_555 L MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc14 K O2B ADP . D ADP 1001 1_555 L MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc15 K O2A ADP . D ADP 1001 1_555 L MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? # _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 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 4RIW _atom_sites.fract_transf_matrix[1][1] 0.015202 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005802 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006467 _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] 0.012307 _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 E 3 ANP A 1 1101 1 ANP ANP . F 4 MG A 1 1102 2 MG MG . G 5 ADP B 1 1001 1 ADP ADP . H 4 MG B 1 1002 2 MG MG . I 3 ANP C 1 1101 1 ANP ANP . J 4 MG C 1 1102 2 MG MG . K 5 ADP D 1 1001 1 ADP ADP . L 4 MG D 1 1002 2 MG MG . # 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 . . . G 5 3.621 -4.154 7.973 1 47.2 ? PB ADP 1001 B 1 HETATM 2 O O1B ADP . . . G 5 3.047 -3.563 6.71 1 49.26 ? O1B ADP 1001 B 1 HETATM 3 O O2B ADP . . . G 5 3.635 -3.195 9.139 1 46.51 1 O2B ADP 1001 B 1 HETATM 4 O O3B ADP . . . G 5 3.059 -5.518 8.298 1 50.27 ? O3B ADP 1001 B 1 HETATM 5 P PA ADP . . . G 5 6.09 -3.901 6.496 1 40.11 ? PA ADP 1001 B 1 HETATM 6 O O1A ADP . . . G 5 7.058 -4.99 6.096 1 35.81 1 O1A ADP 1001 B 1 HETATM 7 O O2A ADP . . . G 5 5.249 -3.221 5.444 1 37.23 ? O2A ADP 1001 B 1 HETATM 8 O O3A ADP . . . G 5 5.186 -4.463 7.711 1 17.33 ? O3A ADP 1001 B 1 HETATM 9 O O5' ADP . . . G 5 6.9 -2.713 7.216 1 36.28 ? O5' ADP 1001 B 1 HETATM 10 C C5' ADP . . . G 5 7.166 -1.539 6.454 1 39.49 ? C5' ADP 1001 B 1 HETATM 11 C C4' ADP . . . G 5 7.48 -0.346 7.347 1 35.58 ? C4' ADP 1001 B 1 HETATM 12 O O4' ADP . . . G 5 8.504 -0.698 8.278 1 30.25 ? O4' ADP 1001 B 1 HETATM 13 C C3' ADP . . . G 5 7.987 0.81 6.501 1 32.5 ? C3' ADP 1001 B 1 HETATM 14 O O3' ADP . . . G 5 7.274 2.01 6.815 1 40.16 ? O3' ADP 1001 B 1 HETATM 15 C C2' ADP . . . G 5 9.451 0.961 6.856 1 29.61 ? C2' ADP 1001 B 1 HETATM 16 O O2' ADP . . . G 5 9.728 2.303 7.265 1 39.45 ? O2' ADP 1001 B 1 HETATM 17 C C1' ADP . . . G 5 9.723 -0.012 7.992 1 27.6 ? C1' ADP 1001 B 1 HETATM 18 N N9 ADP . . . G 5 10.689 -1.014 7.488 1 30.24 ? N9 ADP 1001 B 1 HETATM 19 C C8 ADP . . . G 5 10.445 -2.33 7.332 1 24.17 ? C8 ADP 1001 B 1 HETATM 20 N N7 ADP . . . G 5 11.535 -2.977 6.845 1 17.45 ? N7 ADP 1001 B 1 HETATM 21 C C5 ADP . . . G 5 12.504 -2.058 6.681 1 24.54 ? C5 ADP 1001 B 1 HETATM 22 C C6 ADP . . . G 5 13.906 -2.059 6.201 1 30.85 ? C6 ADP 1001 B 1 HETATM 23 N N6 ADP . . . G 5 14.503 -3.205 5.793 1 29.44 ? N6 ADP 1001 B 1 HETATM 24 N N1 ADP . . . G 5 14.569 -0.882 6.191 1 37.79 ? N1 ADP 1001 B 1 HETATM 25 C C2 ADP . . . G 5 13.988 0.263 6.594 1 38.26 ? C2 ADP 1001 B 1 HETATM 26 N N3 ADP . . . G 5 12.721 0.339 7.04 1 37.26 ? N3 ADP 1001 B 1 HETATM 27 C C4 ADP . . . G 5 11.942 -0.767 7.107 1 31.59 ? C4 ADP 1001 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #