data_5X06 # _model_server_result.job_id EoHuFafnacvlQNpFuTFc_g _model_server_result.datetime_utc '2024-11-25 12:37:49' _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 5x06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":1001}' # _entry.id 5X06 # _exptl.entry_id 5X06 _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 "ADENOSINE-5'-DIPHOSPHATE" _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 90 _cell.entry_id 5X06 _cell.length_a 102.112 _cell.length_b 149.542 _cell.length_c 200.78 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X06 _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 K N N ? 4 N N N ? 4 P N N ? 4 S 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 E OG SER 77 E SER 57 1_555 L MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc2 K O1B ADP . E ADP 1001 1_555 L MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc3 K O1A ADP . E ADP 1001 1_555 L MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc4 L MG MG . E MG 1002 1_555 Y O HOH . E HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc5 F OG SER 77 F SER 57 1_555 O MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc6 N O3B ADP . F ADP 1001 1_555 O MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc7 O MG MG . F MG 1002 1_555 Z O HOH . F HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc8 G OG SER 77 G SER 57 1_555 Q MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? metalc ? metalc9 P O1B ADP . G ADP 1001 1_555 Q MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc10 P O1A ADP . G ADP 1001 1_555 Q MG MG . G MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc11 Q MG MG . G MG 1002 1_555 AA O HOH . G HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc12 H OG SER 77 H SER 57 1_555 T MG MG . H MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc13 T MG MG . H MG 1002 1_555 BA O HOH . H HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? # _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 5X06 _atom_sites.fract_transf_matrix[1][1] 0.009793 _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] 0.006687 _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] 0.004981 _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 I 3 GOL C 1 401 4 GOL GOL . J 3 GOL D 1 401 3 GOL GOL . K 4 ADP E 1 1001 1001 ADP ADP . L 5 MG E 1 1002 1002 MG MG . M 3 GOL E 1 1003 1 GOL GOL . N 4 ADP F 1 1001 1001 ADP ADP . O 5 MG F 1 1002 1002 MG MG . P 4 ADP G 1 1001 1001 ADP ADP . Q 5 MG G 1 1002 1002 MG MG . R 3 GOL G 1 1003 2 GOL GOL . S 4 ADP H 1 1001 1001 ADP ADP . T 5 MG H 1 1002 1002 MG MG . U 6 HOH A 1 401 2 HOH HOH . U 6 HOH A 2 402 12 HOH HOH . U 6 HOH A 3 403 14 HOH HOH . U 6 HOH A 4 404 4 HOH HOH . U 6 HOH A 5 405 3 HOH HOH . V 6 HOH B 1 401 13 HOH HOH . V 6 HOH B 2 402 22 HOH HOH . V 6 HOH B 3 403 1 HOH HOH . V 6 HOH B 4 404 11 HOH HOH . W 6 HOH C 1 501 27 HOH HOH . W 6 HOH C 2 502 28 HOH HOH . W 6 HOH C 3 503 10 HOH HOH . W 6 HOH C 4 504 7 HOH HOH . W 6 HOH C 5 505 29 HOH HOH . W 6 HOH C 6 506 8 HOH HOH . X 6 HOH D 1 501 26 HOH HOH . X 6 HOH D 2 502 24 HOH HOH . X 6 HOH D 3 503 6 HOH HOH . X 6 HOH D 4 504 30 HOH HOH . X 6 HOH D 5 505 9 HOH HOH . Y 6 HOH E 1 1101 19 HOH HOH . Y 6 HOH E 2 1102 25 HOH HOH . Y 6 HOH E 3 1103 5 HOH HOH . Z 6 HOH F 1 1101 23 HOH HOH . Z 6 HOH F 2 1102 20 HOH HOH . Z 6 HOH F 3 1103 21 HOH HOH . AA 6 HOH G 1 1101 17 HOH HOH . AA 6 HOH G 2 1102 18 HOH HOH . BA 6 HOH H 1 1101 15 HOH HOH . BA 6 HOH H 2 1102 16 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 . . . P 4 -55.273 -48.605 51.373 1 155.16 ? PB ADP 1001 G 1 HETATM 2 O O1B ADP . . . P 4 -55.651 -49.69 50.394 1 154.5 ? O1B ADP 1001 G 1 HETATM 3 O O2B ADP . . . P 4 -55.824 -47.238 51.053 1 152.44 ? O2B ADP 1001 G 1 HETATM 4 O O3B ADP . . . P 4 -53.814 -48.603 51.759 1 151.68 ? O3B ADP 1001 G 1 HETATM 5 P PA ADP . . . P 4 -55.677 -50.302 53.574 1 180.38 ? PA ADP 1001 G 1 HETATM 6 O O1A ADP . . . P 4 -56.157 -51.525 52.829 1 184.86 ? O1A ADP 1001 G 1 HETATM 7 O O2A ADP . . . P 4 -54.23 -50.172 53.982 1 181.34 ? O2A ADP 1001 G 1 HETATM 8 O O3A ADP . . . P 4 -56.062 -48.997 52.719 1 169.89 ? O3A ADP 1001 G 1 HETATM 9 O O5' ADP . . . P 4 -56.585 -50.083 54.884 1 181.74 ? O5' ADP 1001 G 1 HETATM 10 C C5' ADP . . . P 4 -55.992 -49.535 56.06 1 171.43 ? C5' ADP 1001 G 1 HETATM 11 C C4' ADP . . . P 4 -56.934 -49.662 57.25 1 159.55 ? C4' ADP 1001 G 1 HETATM 12 O O4' ADP . . . P 4 -56.865 -48.48 58.054 1 153.04 ? O4' ADP 1001 G 1 HETATM 13 C C3' ADP . . . P 4 -58.383 -49.83 56.828 1 153.75 ? C3' ADP 1001 G 1 HETATM 14 O O3' ADP . . . P 4 -58.797 -51.184 57.028 1 155.74 ? O3' ADP 1001 G 1 HETATM 15 C C2' ADP . . . P 4 -59.179 -48.906 57.726 1 147.32 ? C2' ADP 1001 G 1 HETATM 16 O O2' ADP . . . P 4 -59.981 -49.675 58.627 1 144.86 ? O2' ADP 1001 G 1 HETATM 17 C C1' ADP . . . P 4 -58.163 -48.092 58.511 1 146.81 ? C1' ADP 1001 G 1 HETATM 18 N N9 ADP . . . P 4 -58.382 -46.651 58.229 1 141.16 ? N9 ADP 1001 G 1 HETATM 19 C C8 ADP . . . P 4 -57.568 -45.865 57.5 1 139.04 ? C8 ADP 1001 G 1 HETATM 20 N N7 ADP . . . P 4 -58.045 -44.596 57.427 1 136.98 ? N7 ADP 1001 G 1 HETATM 21 C C5 ADP . . . P 4 -59.194 -44.556 58.125 1 135.79 ? C5 ADP 1001 G 1 HETATM 22 C C6 ADP . . . P 4 -60.208 -43.525 58.452 1 135.09 ? C6 ADP 1001 G 1 HETATM 23 N N6 ADP . . . P 4 -60.083 -42.251 58.005 1 135.46 ? N6 ADP 1001 G 1 HETATM 24 N N1 ADP . . . P 4 -61.261 -43.899 59.211 1 134.25 ? N1 ADP 1001 G 1 HETATM 25 C C2 ADP . . . P 4 -61.396 -45.16 59.659 1 135.41 ? C2 ADP 1001 G 1 HETATM 26 N N3 ADP . . . P 4 -60.517 -46.145 59.401 1 137.4 ? N3 ADP 1001 G 1 HETATM 27 C C4 ADP . . . P 4 -59.412 -45.911 58.653 1 137.71 ? C4 ADP 1001 G 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 27 #