data_4J8F # _model_server_result.job_id jCmHDFyGGs7sbHayTdcZsA _model_server_result.datetime_utc '2024-10-19 03:37:03' _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 4j8f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 4J8F # _exptl.entry_id 4J8F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 4J8F _cell.length_a 65.596 _cell.length_b 65.596 _cell.length_c 141.47 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4J8F _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA monomeric 1 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,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V 1 1,2 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_555 -y,x,z+1/4 0 -1 0 1 0 0 0 0 1 0 0 35.3675 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 metalc ? metalc1 B O2B ADP . A ADP 601 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? metalc ? metalc2 C MG MG . A MG 602 1_555 D O3 PO4 . A PO4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc3 C MG MG . A MG 602 1_555 V O HOH . A HOH 722 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc4 C MG MG . A MG 602 1_555 V O HOH . A HOH 723 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc5 C MG MG . A MG 602 1_555 V O HOH . A HOH 724 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc6 C MG MG . A MG 602 1_555 V O HOH . A HOH 725 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? # _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 4J8F _atom_sites.fract_transf_matrix[1][1] 0.015245 _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] 0.015245 _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] 0.007069 _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 B 2 ADP A 1 601 600 ADP ADP . C 3 MG A 1 602 650 MG MG . D 4 PO4 A 1 603 700 PO4 PO4 . E 5 IOD A 1 604 1 IOD IOD . F 5 IOD A 1 605 2 IOD IOD . G 5 IOD A 1 606 3 IOD IOD . H 5 IOD A 1 607 4 IOD IOD . I 5 IOD A 1 608 5 IOD IOD . J 5 IOD A 1 609 6 IOD IOD . K 5 IOD A 1 610 7 IOD IOD . L 5 IOD A 1 611 8 IOD IOD . M 5 IOD A 1 612 9 IOD IOD . N 5 IOD A 1 613 10 IOD IOD . O 5 IOD A 1 614 11 IOD IOD . P 5 IOD A 1 615 12 IOD IOD . Q 5 IOD A 1 616 13 IOD IOD . R 5 IOD A 1 617 14 IOD IOD . S 5 IOD A 1 618 15 IOD IOD . T 5 IOD A 1 619 16 IOD IOD . U 5 IOD A 1 620 17 IOD IOD . V 6 HOH A 1 701 1 HOH HOH . V 6 HOH A 2 702 2 HOH HOH . V 6 HOH A 3 703 3 HOH HOH . V 6 HOH A 4 704 4 HOH HOH . V 6 HOH A 5 705 5 HOH HOH . V 6 HOH A 6 706 6 HOH HOH . V 6 HOH A 7 707 7 HOH HOH . V 6 HOH A 8 708 8 HOH HOH . V 6 HOH A 9 709 9 HOH HOH . V 6 HOH A 10 710 10 HOH HOH . V 6 HOH A 11 711 11 HOH HOH . V 6 HOH A 12 712 12 HOH HOH . V 6 HOH A 13 713 13 HOH HOH . V 6 HOH A 14 714 14 HOH HOH . V 6 HOH A 15 715 15 HOH HOH . V 6 HOH A 16 716 16 HOH HOH . V 6 HOH A 17 717 17 HOH HOH . V 6 HOH A 18 718 18 HOH HOH . V 6 HOH A 19 719 19 HOH HOH . V 6 HOH A 20 720 20 HOH HOH . V 6 HOH A 21 721 21 HOH HOH . V 6 HOH A 22 722 22 HOH HOH . V 6 HOH A 23 723 23 HOH HOH . V 6 HOH A 24 724 24 HOH HOH . V 6 HOH A 25 725 25 HOH HOH . V 6 HOH A 26 726 26 HOH HOH . V 6 HOH A 27 727 27 HOH HOH . V 6 HOH A 28 728 28 HOH HOH . V 6 HOH A 29 729 29 HOH HOH . V 6 HOH A 30 730 30 HOH HOH . V 6 HOH A 31 731 31 HOH HOH . V 6 HOH A 32 732 32 HOH HOH . V 6 HOH A 33 733 33 HOH HOH . V 6 HOH A 34 734 34 HOH HOH . V 6 HOH A 35 735 35 HOH HOH . V 6 HOH A 36 736 36 HOH HOH . V 6 HOH A 37 737 37 HOH HOH . V 6 HOH A 38 738 38 HOH HOH . V 6 HOH A 39 739 39 HOH HOH . V 6 HOH A 40 740 40 HOH HOH . V 6 HOH A 41 741 41 HOH HOH . V 6 HOH A 42 742 42 HOH HOH . V 6 HOH A 43 743 43 HOH HOH . V 6 HOH A 44 744 44 HOH HOH . V 6 HOH A 45 745 45 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 . . . B 2 19.581 0.149 -0.259 1 35.58 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . B 2 19.516 1.651 -0.065 1 33.46 ? O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . B 2 18.525 -0.613 0.502 1 36.79 ? O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . B 2 20.948 -0.5 -0.171 1 33.71 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . B 2 19.267 -1.398 -2.676 1 33.82 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . B 2 18.923 -2.615 -1.826 1 32.34 ? O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . B 2 18.415 -1.114 -3.894 1 33.57 ? O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . B 2 19.193 -0.032 -1.807 1 34.16 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . B 2 20.804 -1.404 -3.172 1 31.84 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . B 2 21.283 -0.377 -4.057 1 33.12 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . B 2 22.634 -0.787 -4.645 1 35.17 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . B 2 22.505 -1.982 -5.436 1 35.54 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . B 2 23.272 0.283 -5.518 1 35.32 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . B 2 24.634 0.481 -5.122 1 35.02 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . B 2 23.271 -0.354 -6.895 1 36.23 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . B 2 24.439 -0.022 -7.655 1 37.82 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . B 2 23.238 -1.842 -6.637 1 34.95 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . B 2 22.559 -2.51 -7.761 1 35.75 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . B 2 21.254 -2.428 -8.081 1 36.01 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . B 2 20.984 -3.165 -9.192 1 36.58 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . B 2 22.131 -3.731 -9.598 1 35.83 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . B 2 22.554 -4.621 -10.701 1 37.19 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . B 2 21.676 -5.083 -11.616 1 38.03 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . B 2 23.86 -4.965 -10.762 1 38.4 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . B 2 24.756 -4.517 -9.855 1 38.19 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . B 2 24.441 -3.701 -8.828 1 36 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . B 2 23.168 -3.287 -8.655 1 35.48 ? C4 ADP 601 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #