data_5L8J # _model_server_result.job_id 1nGCxyKMR4NdbIzWUBE6IA _model_server_result.datetime_utc '2024-10-10 03:23:51' _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 5l8j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5L8J # _exptl.entry_id 5L8J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 5L8J _cell.length_a 91.23 _cell.length_b 111.12 _cell.length_c 41.62 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L8J _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _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 disulf ? disulf1 B SG CYS 23 B CYS 23 1_555 B SG CYS 84 B CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf2 B SG CYS 30 B CYS 30 1_555 B SG CYS 90 B CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? # _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 5L8J _atom_sites.fract_transf_matrix[1][1] 0.010961 _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] 0.008999 _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] 0.024027 _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 3 ADP A 1 501 1 ADP ADP . D 4 EDO A 1 502 2 EDO EDO . E 4 EDO A 1 503 3 EDO EDO . F 5 PEG A 1 504 4 PEG PEG . G 5 PEG A 1 505 5 PEG PEG . H 6 HOH A 1 601 128 HOH HOH . H 6 HOH A 2 602 29 HOH HOH . H 6 HOH A 3 603 136 HOH HOH . H 6 HOH A 4 604 197 HOH HOH . H 6 HOH A 5 605 146 HOH HOH . H 6 HOH A 6 606 143 HOH HOH . H 6 HOH A 7 607 26 HOH HOH . H 6 HOH A 8 608 93 HOH HOH . H 6 HOH A 9 609 18 HOH HOH . H 6 HOH A 10 610 60 HOH HOH . H 6 HOH A 11 611 19 HOH HOH . H 6 HOH A 12 612 42 HOH HOH . H 6 HOH A 13 613 156 HOH HOH . H 6 HOH A 14 614 11 HOH HOH . H 6 HOH A 15 615 36 HOH HOH . H 6 HOH A 16 616 75 HOH HOH . H 6 HOH A 17 617 123 HOH HOH . H 6 HOH A 18 618 105 HOH HOH . H 6 HOH A 19 619 16 HOH HOH . H 6 HOH A 20 620 109 HOH HOH . H 6 HOH A 21 621 13 HOH HOH . H 6 HOH A 22 622 110 HOH HOH . H 6 HOH A 23 623 140 HOH HOH . H 6 HOH A 24 624 8 HOH HOH . H 6 HOH A 25 625 104 HOH HOH . H 6 HOH A 26 626 72 HOH HOH . H 6 HOH A 27 627 30 HOH HOH . H 6 HOH A 28 628 85 HOH HOH . H 6 HOH A 29 629 149 HOH HOH . H 6 HOH A 30 630 52 HOH HOH . H 6 HOH A 31 631 48 HOH HOH . H 6 HOH A 32 632 184 HOH HOH . H 6 HOH A 33 633 3 HOH HOH . H 6 HOH A 34 634 50 HOH HOH . H 6 HOH A 35 635 35 HOH HOH . H 6 HOH A 36 636 12 HOH HOH . H 6 HOH A 37 637 81 HOH HOH . H 6 HOH A 38 638 25 HOH HOH . H 6 HOH A 39 639 22 HOH HOH . H 6 HOH A 40 640 32 HOH HOH . H 6 HOH A 41 641 27 HOH HOH . H 6 HOH A 42 642 100 HOH HOH . H 6 HOH A 43 643 130 HOH HOH . H 6 HOH A 44 644 20 HOH HOH . H 6 HOH A 45 645 66 HOH HOH . H 6 HOH A 46 646 28 HOH HOH . H 6 HOH A 47 647 37 HOH HOH . H 6 HOH A 48 648 1 HOH HOH . H 6 HOH A 49 649 139 HOH HOH . H 6 HOH A 50 650 24 HOH HOH . H 6 HOH A 51 651 14 HOH HOH . H 6 HOH A 52 652 51 HOH HOH . H 6 HOH A 53 653 121 HOH HOH . H 6 HOH A 54 654 2 HOH HOH . H 6 HOH A 55 655 148 HOH HOH . H 6 HOH A 56 656 57 HOH HOH . H 6 HOH A 57 657 10 HOH HOH . H 6 HOH A 58 658 124 HOH HOH . H 6 HOH A 59 659 112 HOH HOH . H 6 HOH A 60 660 157 HOH HOH . H 6 HOH A 61 661 59 HOH HOH . H 6 HOH A 62 662 62 HOH HOH . H 6 HOH A 63 663 137 HOH HOH . H 6 HOH A 64 664 187 HOH HOH . H 6 HOH A 65 665 21 HOH HOH . H 6 HOH A 66 666 6 HOH HOH . H 6 HOH A 67 667 45 HOH HOH . H 6 HOH A 68 668 170 HOH HOH . H 6 HOH A 69 669 31 HOH HOH . H 6 HOH A 70 670 33 HOH HOH . H 6 HOH A 71 671 5 HOH HOH . H 6 HOH A 72 672 17 HOH HOH . H 6 HOH A 73 673 171 HOH HOH . H 6 HOH A 74 674 65 HOH HOH . H 6 HOH A 75 675 169 HOH HOH . H 6 HOH A 76 676 84 HOH HOH . H 6 HOH A 77 677 113 HOH HOH . H 6 HOH A 78 678 135 HOH HOH . H 6 HOH A 79 679 155 HOH HOH . H 6 HOH A 80 680 61 HOH HOH . H 6 HOH A 81 681 41 HOH HOH . H 6 HOH A 82 682 88 HOH HOH . H 6 HOH A 83 683 74 HOH HOH . H 6 HOH A 84 684 125 HOH HOH . H 6 HOH A 85 685 153 HOH HOH . H 6 HOH A 86 686 23 HOH HOH . H 6 HOH A 87 687 43 HOH HOH . H 6 HOH A 88 688 162 HOH HOH . H 6 HOH A 89 689 82 HOH HOH . H 6 HOH A 90 690 108 HOH HOH . H 6 HOH A 91 691 47 HOH HOH . H 6 HOH A 92 692 154 HOH HOH . H 6 HOH A 93 693 167 HOH HOH . H 6 HOH A 94 694 134 HOH HOH . H 6 HOH A 95 695 34 HOH HOH . H 6 HOH A 96 696 138 HOH HOH . H 6 HOH A 97 697 56 HOH HOH . H 6 HOH A 98 698 116 HOH HOH . H 6 HOH A 99 699 38 HOH HOH . H 6 HOH A 100 700 91 HOH HOH . H 6 HOH A 101 701 64 HOH HOH . H 6 HOH A 102 702 192 HOH HOH . H 6 HOH A 103 703 122 HOH HOH . H 6 HOH A 104 704 183 HOH HOH . H 6 HOH A 105 705 166 HOH HOH . H 6 HOH A 106 706 95 HOH HOH . H 6 HOH A 107 707 107 HOH HOH . H 6 HOH A 108 708 69 HOH HOH . H 6 HOH A 109 709 49 HOH HOH . H 6 HOH A 110 710 131 HOH HOH . H 6 HOH A 111 711 53 HOH HOH . H 6 HOH A 112 712 44 HOH HOH . H 6 HOH A 113 713 173 HOH HOH . H 6 HOH A 114 714 179 HOH HOH . H 6 HOH A 115 715 83 HOH HOH . H 6 HOH A 116 716 185 HOH HOH . H 6 HOH A 117 717 141 HOH HOH . H 6 HOH A 118 718 175 HOH HOH . H 6 HOH A 119 719 191 HOH HOH . H 6 HOH A 120 720 150 HOH HOH . H 6 HOH A 121 721 77 HOH HOH . H 6 HOH A 122 722 186 HOH HOH . H 6 HOH A 123 723 120 HOH HOH . H 6 HOH A 124 724 126 HOH HOH . H 6 HOH A 125 725 98 HOH HOH . H 6 HOH A 126 726 164 HOH HOH . H 6 HOH A 127 727 142 HOH HOH . H 6 HOH A 128 728 79 HOH HOH . H 6 HOH A 129 729 172 HOH HOH . H 6 HOH A 130 730 193 HOH HOH . H 6 HOH A 131 731 168 HOH HOH . H 6 HOH A 132 732 92 HOH HOH . H 6 HOH A 133 733 133 HOH HOH . H 6 HOH A 134 734 189 HOH HOH . H 6 HOH A 135 735 161 HOH HOH . H 6 HOH A 136 736 188 HOH HOH . H 6 HOH A 137 737 174 HOH HOH . H 6 HOH A 138 738 196 HOH HOH . H 6 HOH A 139 739 190 HOH HOH . I 6 HOH B 1 201 158 HOH HOH . I 6 HOH B 2 202 80 HOH HOH . I 6 HOH B 3 203 117 HOH HOH . I 6 HOH B 4 204 181 HOH HOH . I 6 HOH B 5 205 87 HOH HOH . I 6 HOH B 6 206 163 HOH HOH . I 6 HOH B 7 207 99 HOH HOH . I 6 HOH B 8 208 15 HOH HOH . I 6 HOH B 9 209 40 HOH HOH . I 6 HOH B 10 210 68 HOH HOH . I 6 HOH B 11 211 78 HOH HOH . I 6 HOH B 12 212 4 HOH HOH . I 6 HOH B 13 213 55 HOH HOH . I 6 HOH B 14 214 71 HOH HOH . I 6 HOH B 15 215 46 HOH HOH . I 6 HOH B 16 216 89 HOH HOH . I 6 HOH B 17 217 54 HOH HOH . I 6 HOH B 18 218 7 HOH HOH . I 6 HOH B 19 219 39 HOH HOH . I 6 HOH B 20 220 106 HOH HOH . I 6 HOH B 21 221 132 HOH HOH . I 6 HOH B 22 222 63 HOH HOH . I 6 HOH B 23 223 114 HOH HOH . I 6 HOH B 24 224 152 HOH HOH . I 6 HOH B 25 225 102 HOH HOH . I 6 HOH B 26 226 96 HOH HOH . I 6 HOH B 27 227 94 HOH HOH . I 6 HOH B 28 228 97 HOH HOH . I 6 HOH B 29 229 9 HOH HOH . I 6 HOH B 30 230 165 HOH HOH . I 6 HOH B 31 231 67 HOH HOH . I 6 HOH B 32 232 73 HOH HOH . I 6 HOH B 33 233 58 HOH HOH . I 6 HOH B 34 234 119 HOH HOH . I 6 HOH B 35 235 101 HOH HOH . I 6 HOH B 36 236 151 HOH HOH . I 6 HOH B 37 237 127 HOH HOH . I 6 HOH B 38 238 86 HOH HOH . I 6 HOH B 39 239 76 HOH HOH . I 6 HOH B 40 240 147 HOH HOH . I 6 HOH B 41 241 103 HOH HOH . I 6 HOH B 42 242 159 HOH HOH . I 6 HOH B 43 243 144 HOH HOH . I 6 HOH B 44 244 70 HOH HOH . I 6 HOH B 45 245 129 HOH HOH . I 6 HOH B 46 246 115 HOH HOH . I 6 HOH B 47 247 118 HOH HOH . I 6 HOH B 48 248 145 HOH HOH . I 6 HOH B 49 249 160 HOH HOH . I 6 HOH B 50 250 90 HOH HOH . I 6 HOH B 51 251 111 HOH HOH . I 6 HOH B 52 252 195 HOH HOH . I 6 HOH B 53 253 194 HOH HOH . I 6 HOH B 54 254 178 HOH HOH . I 6 HOH B 55 255 177 HOH HOH . I 6 HOH B 56 256 182 HOH HOH . I 6 HOH B 57 257 180 HOH HOH . I 6 HOH B 58 258 176 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 . . . C 3 -17.542 15.19 3.513 1 62.43 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . C 3 -17.137 14.004 2.67 1 63.84 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . C 3 -18.601 16.073 2.897 1 60.61 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . C 3 -17.749 14.866 4.973 1 63.27 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . C 3 -15.772 17.052 2.302 1 56.93 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . C 3 -14.769 16.296 1.472 1 61.59 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . C 3 -16.929 17.747 1.627 1 64.84 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . C 3 -16.238 16.131 3.538 1 62.69 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . C 3 -15.026 18.201 3.14 1 61.55 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . C 3 -13.623 18.296 3.183 1 53.56 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . C 3 -13.256 19.759 3.333 1 47.11 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . C 3 -12.003 19.872 2.669 1 41.43 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . C 3 -14.217 20.71 2.626 1 45.28 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . C 3 -15.018 21.456 3.547 1 59.9 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . C 3 -13.335 21.644 1.833 1 42 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . C 3 -13.051 22.83 2.582 1 52.43 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . C 3 -12.04 20.877 1.668 1 35.41 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . C 3 -12.06 20.209 0.346 1 38.56 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . C 3 -12.735 19.091 0.016 1 39.73 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . C 3 -12.535 18.758 -1.284 1 33.37 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . C 3 -11.71 19.69 -1.794 1 33.03 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . C 3 -11.084 19.943 -3.102 1 27.47 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . C 3 -11.31 19.11 -4.146 1 27 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . C 3 -10.301 21.025 -3.22 1 28.28 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . C 3 -10.05 21.854 -2.193 1 34.87 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . C 3 -10.579 21.681 -0.972 1 35.56 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . C 3 -11.404 20.642 -0.722 1 35.09 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #