data_6G2X # _model_server_result.job_id emv5WMWX1kraq4xImBMH5Q _model_server_result.datetime_utc '2024-11-05 09:29:18' _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 6g2x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":809}' # _entry.id 6G2X # _exptl.entry_id 6G2X _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 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 120 _cell.entry_id 6G2X _cell.length_a 93.282 _cell.length_b 93.282 _cell.length_c 65.997 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6G2X _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id J _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 A OD1 ASN 166 A ASN 624 1_555 K NA NA . A NA 810 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc2 J O3B ADP . A ADP 809 1_555 K NA NA . A NA 810 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.096 ? metalc ? metalc3 K NA NA . A NA 810 1_555 L O HOH . A HOH 972 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.117 ? # _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 6G2X _atom_sites.fract_transf_matrix[1][1] 0.01072 _atom_sites.fract_transf_matrix[1][2] 0.006189 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012379 _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] 0.015152 _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 MPD A 1 801 1 MPD MPD . C 2 MPD A 1 802 2 MPD MPD . D 2 MPD A 1 803 3 MPD MPD . E 2 MPD A 1 804 4 MPD MPD . F 3 DMS A 1 805 5 DMS DMS . G 3 DMS A 1 806 6 DMS DMS . H 4 EJQ A 1 807 7 EJQ LIG . I 4 EJQ A 1 808 8 EJQ LIG . J 5 ADP A 1 809 9 ADP ADP . K 6 NA A 1 810 10 NA NA . L 7 HOH A 1 901 77 HOH HOH . L 7 HOH A 2 902 78 HOH HOH . L 7 HOH A 3 903 60 HOH HOH . L 7 HOH A 4 904 64 HOH HOH . L 7 HOH A 5 905 76 HOH HOH . L 7 HOH A 6 906 28 HOH HOH . L 7 HOH A 7 907 69 HOH HOH . L 7 HOH A 8 908 18 HOH HOH . L 7 HOH A 9 909 25 HOH HOH . L 7 HOH A 10 910 34 HOH HOH . L 7 HOH A 11 911 74 HOH HOH . L 7 HOH A 12 912 21 HOH HOH . L 7 HOH A 13 913 12 HOH HOH . L 7 HOH A 14 914 11 HOH HOH . L 7 HOH A 15 915 47 HOH HOH . L 7 HOH A 16 916 36 HOH HOH . L 7 HOH A 17 917 32 HOH HOH . L 7 HOH A 18 918 22 HOH HOH . L 7 HOH A 19 919 10 HOH HOH . L 7 HOH A 20 920 7 HOH HOH . L 7 HOH A 21 921 27 HOH HOH . L 7 HOH A 22 922 20 HOH HOH . L 7 HOH A 23 923 3 HOH HOH . L 7 HOH A 24 924 46 HOH HOH . L 7 HOH A 25 925 1 HOH HOH . L 7 HOH A 26 926 44 HOH HOH . L 7 HOH A 27 927 6 HOH HOH . L 7 HOH A 28 928 45 HOH HOH . L 7 HOH A 29 929 51 HOH HOH . L 7 HOH A 30 930 4 HOH HOH . L 7 HOH A 31 931 2 HOH HOH . L 7 HOH A 32 932 71 HOH HOH . L 7 HOH A 33 933 48 HOH HOH . L 7 HOH A 34 934 43 HOH HOH . L 7 HOH A 35 935 38 HOH HOH . L 7 HOH A 36 936 37 HOH HOH . L 7 HOH A 37 937 54 HOH HOH . L 7 HOH A 38 938 41 HOH HOH . L 7 HOH A 39 939 42 HOH HOH . L 7 HOH A 40 940 70 HOH HOH . L 7 HOH A 41 941 19 HOH HOH . L 7 HOH A 42 942 29 HOH HOH . L 7 HOH A 43 943 8 HOH HOH . L 7 HOH A 44 944 63 HOH HOH . L 7 HOH A 45 945 9 HOH HOH . L 7 HOH A 46 946 40 HOH HOH . L 7 HOH A 47 947 68 HOH HOH . L 7 HOH A 48 948 50 HOH HOH . L 7 HOH A 49 949 35 HOH HOH . L 7 HOH A 50 950 31 HOH HOH . L 7 HOH A 51 951 66 HOH HOH . L 7 HOH A 52 952 23 HOH HOH . L 7 HOH A 53 953 49 HOH HOH . L 7 HOH A 54 954 5 HOH HOH . L 7 HOH A 55 955 56 HOH HOH . L 7 HOH A 56 956 65 HOH HOH . L 7 HOH A 57 957 13 HOH HOH . L 7 HOH A 58 958 17 HOH HOH . L 7 HOH A 59 959 59 HOH HOH . L 7 HOH A 60 960 30 HOH HOH . L 7 HOH A 61 961 58 HOH HOH . L 7 HOH A 62 962 33 HOH HOH . L 7 HOH A 63 963 62 HOH HOH . L 7 HOH A 64 964 15 HOH HOH . L 7 HOH A 65 965 24 HOH HOH . L 7 HOH A 66 966 72 HOH HOH . L 7 HOH A 67 967 26 HOH HOH . L 7 HOH A 68 968 14 HOH HOH . L 7 HOH A 69 969 73 HOH HOH . L 7 HOH A 70 970 53 HOH HOH . L 7 HOH A 71 971 57 HOH HOH . L 7 HOH A 72 972 39 HOH HOH . L 7 HOH A 73 973 52 HOH HOH . L 7 HOH A 74 974 67 HOH HOH . L 7 HOH A 75 975 61 HOH HOH . L 7 HOH A 76 976 55 HOH HOH . L 7 HOH A 77 977 75 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 . . . J 5 -1.732 -35.741 1.369 1 35.37 ? PB ADP 809 A 1 HETATM 2 O O1B ADP . . . J 5 -0.643 -36.471 0.608 1 35.85 ? O1B ADP 809 A 1 HETATM 3 O O2B ADP . . . J 5 -1.436 -35.632 2.858 1 38.12 ? O2B ADP 809 A 1 HETATM 4 O O3B ADP . . . J 5 -2.174 -34.503 0.63 1 37.84 ? O3B ADP 809 A 1 HETATM 5 P PA ADP . . . J 5 -3.715 -37.553 2.469 1 37.1 ? PA ADP 809 A 1 HETATM 6 O O1A ADP . . . J 5 -2.703 -38.548 2.982 1 32.68 ? O1A ADP 809 A 1 HETATM 7 O O2A ADP . . . J 5 -4.459 -36.621 3.408 1 38.01 ? O2A ADP 809 A 1 HETATM 8 O O3A ADP . . . J 5 -3.034 -36.712 1.28 1 33.94 ? O3A ADP 809 A 1 HETATM 9 O O5' ADP . . . J 5 -4.834 -38.419 1.68 1 32.39 ? O5' ADP 809 A 1 HETATM 10 C C5' ADP . . . J 5 -6.167 -37.919 1.533 1 30.56 ? C5' ADP 809 A 1 HETATM 11 C C4' ADP . . . J 5 -7.181 -39.051 1.482 1 30.09 ? C4' ADP 809 A 1 HETATM 12 O O4' ADP . . . J 5 -7.094 -39.756 0.24 1 36.55 ? O4' ADP 809 A 1 HETATM 13 C C3' ADP . . . J 5 -6.958 -40.115 2.562 1 36.42 ? C3' ADP 809 A 1 HETATM 14 O O3' ADP . . . J 5 -7.716 -39.865 3.743 1 38.44 ? O3' ADP 809 A 1 HETATM 15 C C2' ADP . . . J 5 -7.472 -41.361 1.897 1 36.38 ? C2' ADP 809 A 1 HETATM 16 O O2' ADP . . . J 5 -8.899 -41.358 1.964 1 37.39 ? O2' ADP 809 A 1 HETATM 17 C C1' ADP . . . J 5 -7.109 -41.167 0.436 1 30.95 ? C1' ADP 809 A 1 HETATM 18 N N9 ADP . . . J 5 -5.737 -41.685 0.16 1 30.71 ? N9 ADP 809 A 1 HETATM 19 C C8 ADP . . . J 5 -4.671 -40.971 -0.279 1 32.02 ? C8 ADP 809 A 1 HETATM 20 N N7 ADP . . . J 5 -3.569 -41.758 -0.443 1 28.29 ? N7 ADP 809 A 1 HETATM 21 C C5 ADP . . . J 5 -3.939 -43.005 -0.113 1 28.17 ? C5 ADP 809 A 1 HETATM 22 C C6 ADP . . . J 5 -3.271 -44.316 -0.039 1 30.88 ? C6 ADP 809 A 1 HETATM 23 N N6 ADP . . . J 5 -1.963 -44.454 -0.4 1 28.2 ? N6 ADP 809 A 1 HETATM 24 N N1 ADP . . . J 5 -4.016 -45.363 0.385 1 31.81 ? N1 ADP 809 A 1 HETATM 25 C C2 ADP . . . J 5 -5.321 -45.252 0.732 1 33.12 ? C2 ADP 809 A 1 HETATM 26 N N3 ADP . . . J 5 -5.995 -44.083 0.671 1 33.81 ? N3 ADP 809 A 1 HETATM 27 C C4 ADP . . . J 5 -5.367 -42.954 0.265 1 28.32 ? C4 ADP 809 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #