data_4EBU # _model_server_result.job_id mymLPCEmNA23annIxUVRaw _model_server_result.datetime_utc '2024-11-23 21:20:20' _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 4ebu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4EBU # _exptl.entry_id 4EBU _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 120 _cell.entry_id 4EBU _cell.length_a 94.308 _cell.length_b 94.308 _cell.length_c 82.959 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EBU _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 5_676 x-y+1,-y+2,-z+5/3 1 0 0 0 -1 0 0 0 -1 0 163.346248 138.265 # _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 # _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 4EBU _atom_sites.fract_transf_matrix[1][1] 0.010604 _atom_sites.fract_transf_matrix[1][2] 0.006122 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012244 _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] 0.012054 _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 CL A 1 401 1 CL CL . C 3 ADP A 1 402 1 ADP ADP . D 4 AMP A 1 402 1 AMP AMP . E 5 HOH A 1 501 1 HOH HOH . E 5 HOH A 2 502 2 HOH HOH . E 5 HOH A 3 503 3 HOH HOH . E 5 HOH A 4 504 4 HOH HOH . E 5 HOH A 5 505 5 HOH HOH . E 5 HOH A 6 506 6 HOH HOH . E 5 HOH A 7 507 7 HOH HOH . E 5 HOH A 8 508 8 HOH HOH . E 5 HOH A 9 509 9 HOH HOH . E 5 HOH A 10 510 10 HOH HOH . E 5 HOH A 11 511 11 HOH HOH . E 5 HOH A 12 512 12 HOH HOH . E 5 HOH A 13 513 13 HOH HOH . E 5 HOH A 14 514 14 HOH HOH . E 5 HOH A 15 515 15 HOH HOH . E 5 HOH A 16 516 16 HOH HOH . E 5 HOH A 17 517 17 HOH HOH . E 5 HOH A 18 518 18 HOH HOH . E 5 HOH A 19 519 19 HOH HOH . E 5 HOH A 20 520 20 HOH HOH . E 5 HOH A 21 521 21 HOH HOH . E 5 HOH A 22 522 22 HOH HOH . E 5 HOH A 23 523 23 HOH HOH . E 5 HOH A 24 524 24 HOH HOH . E 5 HOH A 25 525 25 HOH HOH . E 5 HOH A 26 526 26 HOH HOH . E 5 HOH A 27 527 27 HOH HOH . E 5 HOH A 28 528 28 HOH HOH . E 5 HOH A 29 529 29 HOH HOH . E 5 HOH A 30 530 30 HOH HOH . E 5 HOH A 31 531 31 HOH HOH . E 5 HOH A 32 532 32 HOH HOH . E 5 HOH A 33 533 33 HOH HOH . E 5 HOH A 34 534 34 HOH HOH . E 5 HOH A 35 535 35 HOH HOH . E 5 HOH A 36 536 36 HOH HOH . E 5 HOH A 37 537 37 HOH HOH . E 5 HOH A 38 538 38 HOH HOH . E 5 HOH A 39 539 39 HOH HOH . E 5 HOH A 40 540 40 HOH HOH . E 5 HOH A 41 541 41 HOH HOH . E 5 HOH A 42 542 42 HOH HOH . E 5 HOH A 43 543 43 HOH HOH . E 5 HOH A 44 544 44 HOH HOH . E 5 HOH A 45 545 45 HOH HOH . E 5 HOH A 46 546 46 HOH HOH . E 5 HOH A 47 547 47 HOH HOH . E 5 HOH A 48 548 48 HOH HOH . E 5 HOH A 49 549 49 HOH HOH . E 5 HOH A 50 550 50 HOH HOH . E 5 HOH A 51 551 51 HOH HOH . E 5 HOH A 52 552 52 HOH HOH . E 5 HOH A 53 553 53 HOH HOH . E 5 HOH A 54 554 54 HOH HOH . E 5 HOH A 55 555 55 HOH HOH . E 5 HOH A 56 556 56 HOH HOH . E 5 HOH A 57 557 57 HOH HOH . E 5 HOH A 58 558 58 HOH HOH . E 5 HOH A 59 559 59 HOH HOH . E 5 HOH A 60 560 60 HOH HOH . E 5 HOH A 61 561 61 HOH HOH . E 5 HOH A 62 562 62 HOH HOH . E 5 HOH A 63 563 63 HOH HOH . E 5 HOH A 64 564 64 HOH HOH . E 5 HOH A 65 565 65 HOH HOH . E 5 HOH A 66 566 66 HOH HOH . E 5 HOH A 67 567 67 HOH HOH . E 5 HOH A 68 568 68 HOH HOH . E 5 HOH A 69 569 69 HOH HOH . E 5 HOH A 70 570 70 HOH HOH . E 5 HOH A 71 571 71 HOH HOH . E 5 HOH A 72 572 72 HOH HOH . E 5 HOH A 73 573 73 HOH HOH . E 5 HOH A 74 574 74 HOH HOH . E 5 HOH A 75 575 75 HOH HOH . E 5 HOH A 76 576 76 HOH HOH . E 5 HOH A 77 577 77 HOH HOH . E 5 HOH A 78 578 78 HOH HOH . E 5 HOH A 79 579 79 HOH HOH . E 5 HOH A 80 580 80 HOH HOH . E 5 HOH A 81 581 81 HOH HOH . E 5 HOH A 82 582 82 HOH HOH . E 5 HOH A 83 583 83 HOH HOH . E 5 HOH A 84 584 84 HOH HOH . E 5 HOH A 85 585 85 HOH HOH . E 5 HOH A 86 586 86 HOH HOH . E 5 HOH A 87 587 87 HOH HOH . E 5 HOH A 88 588 88 HOH HOH . E 5 HOH A 89 589 89 HOH HOH . E 5 HOH A 90 590 90 HOH HOH . E 5 HOH A 91 591 91 HOH HOH . E 5 HOH A 92 592 92 HOH HOH . E 5 HOH A 93 593 93 HOH HOH . E 5 HOH A 94 594 94 HOH HOH . E 5 HOH A 95 595 95 HOH HOH . E 5 HOH A 96 596 96 HOH HOH . E 5 HOH A 97 597 97 HOH HOH . E 5 HOH A 98 598 98 HOH HOH . E 5 HOH A 99 599 99 HOH HOH . E 5 HOH A 100 600 100 HOH HOH . E 5 HOH A 101 601 101 HOH HOH . E 5 HOH A 102 602 102 HOH HOH . E 5 HOH A 103 603 103 HOH HOH . E 5 HOH A 104 604 104 HOH HOH . E 5 HOH A 105 605 105 HOH HOH . E 5 HOH A 106 606 106 HOH HOH . E 5 HOH A 107 607 107 HOH HOH . E 5 HOH A 108 608 108 HOH HOH . E 5 HOH A 109 609 109 HOH HOH . E 5 HOH A 110 610 110 HOH HOH . E 5 HOH A 111 611 111 HOH HOH . E 5 HOH A 112 612 112 HOH HOH . E 5 HOH A 113 613 113 HOH HOH . E 5 HOH A 114 614 114 HOH HOH . E 5 HOH A 115 615 115 HOH HOH . E 5 HOH A 116 616 116 HOH HOH . E 5 HOH A 117 617 117 HOH HOH . E 5 HOH A 118 618 118 HOH HOH . E 5 HOH A 119 619 119 HOH HOH . E 5 HOH A 120 620 120 HOH HOH . E 5 HOH A 121 621 121 HOH HOH . E 5 HOH A 122 622 122 HOH HOH . E 5 HOH A 123 623 123 HOH HOH . E 5 HOH A 124 624 124 HOH HOH . E 5 HOH A 125 625 125 HOH HOH . E 5 HOH A 126 626 126 HOH HOH . E 5 HOH A 127 627 127 HOH HOH . E 5 HOH A 128 628 128 HOH HOH . E 5 HOH A 129 629 129 HOH HOH . E 5 HOH A 130 630 130 HOH HOH . E 5 HOH A 131 631 131 HOH HOH . E 5 HOH A 132 632 132 HOH HOH . E 5 HOH A 133 633 133 HOH HOH . E 5 HOH A 134 634 134 HOH HOH . E 5 HOH A 135 635 135 HOH HOH . E 5 HOH A 136 636 136 HOH HOH . E 5 HOH A 137 637 137 HOH HOH . E 5 HOH A 138 638 138 HOH HOH . E 5 HOH A 139 639 139 HOH HOH . E 5 HOH A 140 640 140 HOH HOH . E 5 HOH A 141 641 141 HOH HOH . E 5 HOH A 142 642 142 HOH HOH . E 5 HOH A 143 643 143 HOH HOH . E 5 HOH A 144 644 144 HOH HOH . E 5 HOH A 145 645 145 HOH HOH . E 5 HOH A 146 646 146 HOH HOH . E 5 HOH A 147 647 147 HOH HOH . E 5 HOH A 148 648 148 HOH HOH . E 5 HOH A 149 649 149 HOH HOH . E 5 HOH A 150 650 150 HOH HOH . E 5 HOH A 151 651 151 HOH HOH . E 5 HOH A 152 652 152 HOH HOH . E 5 HOH A 153 653 153 HOH HOH . E 5 HOH A 154 654 154 HOH HOH . E 5 HOH A 155 655 155 HOH HOH . E 5 HOH A 156 656 156 HOH HOH . E 5 HOH A 157 657 157 HOH HOH . E 5 HOH A 158 658 158 HOH HOH . E 5 HOH A 159 659 159 HOH HOH . E 5 HOH A 160 660 160 HOH HOH . E 5 HOH A 161 661 161 HOH HOH . E 5 HOH A 162 662 162 HOH HOH . E 5 HOH A 163 663 163 HOH HOH . E 5 HOH A 164 664 164 HOH HOH . E 5 HOH A 165 665 165 HOH HOH . E 5 HOH A 166 666 166 HOH HOH . E 5 HOH A 167 667 167 HOH HOH . E 5 HOH A 168 668 168 HOH HOH . E 5 HOH A 169 669 169 HOH HOH . E 5 HOH A 170 670 170 HOH HOH . E 5 HOH A 171 671 171 HOH HOH . E 5 HOH A 172 672 172 HOH HOH . E 5 HOH A 173 673 173 HOH HOH . E 5 HOH A 174 674 174 HOH HOH . E 5 HOH A 175 675 175 HOH HOH . E 5 HOH A 176 676 176 HOH HOH . E 5 HOH A 177 677 177 HOH HOH . E 5 HOH A 178 678 178 HOH HOH . E 5 HOH A 179 679 179 HOH HOH . E 5 HOH A 180 680 180 HOH HOH . E 5 HOH A 181 681 181 HOH HOH . E 5 HOH A 182 682 182 HOH HOH . E 5 HOH A 183 683 183 HOH HOH . E 5 HOH A 184 684 184 HOH HOH . E 5 HOH A 185 685 185 HOH HOH . E 5 HOH A 186 686 186 HOH HOH . E 5 HOH A 187 687 187 HOH HOH . E 5 HOH A 188 688 188 HOH HOH . E 5 HOH A 189 689 189 HOH HOH . E 5 HOH A 190 690 191 HOH HOH . E 5 HOH A 191 691 192 HOH HOH . E 5 HOH A 192 692 193 HOH HOH . E 5 HOH A 193 693 194 HOH HOH . E 5 HOH A 194 694 195 HOH HOH . E 5 HOH A 195 695 196 HOH HOH . E 5 HOH A 196 696 197 HOH HOH . E 5 HOH A 197 697 198 HOH HOH . E 5 HOH A 198 698 199 HOH HOH . E 5 HOH A 199 699 200 HOH HOH . E 5 HOH A 200 700 201 HOH HOH . E 5 HOH A 201 701 202 HOH HOH . E 5 HOH A 202 702 203 HOH HOH . E 5 HOH A 203 703 204 HOH HOH . E 5 HOH A 204 704 205 HOH HOH . E 5 HOH A 205 705 206 HOH HOH . E 5 HOH A 206 706 207 HOH HOH . E 5 HOH A 207 707 208 HOH HOH . E 5 HOH A 208 708 209 HOH HOH . E 5 HOH A 209 709 210 HOH HOH . E 5 HOH A 210 710 211 HOH HOH . E 5 HOH A 211 711 212 HOH HOH . E 5 HOH A 212 712 213 HOH HOH . E 5 HOH A 213 713 214 HOH HOH . E 5 HOH A 214 714 215 HOH HOH . E 5 HOH A 215 715 216 HOH HOH . E 5 HOH A 216 716 217 HOH HOH . E 5 HOH A 217 717 218 HOH HOH . E 5 HOH A 218 718 219 HOH HOH . E 5 HOH A 219 719 220 HOH HOH . E 5 HOH A 220 720 222 HOH HOH . E 5 HOH A 221 721 223 HOH HOH . E 5 HOH A 222 722 224 HOH HOH . E 5 HOH A 223 723 225 HOH HOH . E 5 HOH A 224 724 227 HOH HOH . E 5 HOH A 225 725 228 HOH HOH . E 5 HOH A 226 726 232 HOH HOH . E 5 HOH A 227 727 234 HOH HOH . E 5 HOH A 228 728 235 HOH HOH . E 5 HOH A 229 729 236 HOH HOH . E 5 HOH A 230 730 242 HOH HOH . E 5 HOH A 231 731 244 HOH HOH . E 5 HOH A 232 732 245 HOH HOH . E 5 HOH A 233 733 246 HOH HOH . E 5 HOH A 234 734 247 HOH HOH . E 5 HOH A 235 735 248 HOH HOH . E 5 HOH A 236 736 249 HOH HOH . E 5 HOH A 237 737 250 HOH HOH . E 5 HOH A 238 738 251 HOH HOH . E 5 HOH A 239 739 252 HOH HOH . E 5 HOH A 240 740 253 HOH HOH . E 5 HOH A 241 741 254 HOH HOH . E 5 HOH A 242 742 255 HOH HOH . E 5 HOH A 243 743 256 HOH HOH . E 5 HOH A 244 744 257 HOH HOH . E 5 HOH A 245 745 258 HOH HOH . E 5 HOH A 246 746 259 HOH HOH . E 5 HOH A 247 747 261 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 . C 3 81.575 64.68 85.607 0.5 37.8 ? PB ADP 402 A 1 HETATM 2 O O1B ADP . B . C 3 80.652 63.886 84.713 0.5 42.29 ? O1B ADP 402 A 1 HETATM 3 O O2B ADP . B . C 3 81.26 66.159 85.663 0.5 26.46 ? O2B ADP 402 A 1 HETATM 4 O O3B ADP . B . C 3 83.031 64.357 85.386 0.5 33.66 ? O3B ADP 402 A 1 HETATM 5 P PA ADP . B . C 3 81.68 62.722 87.663 0.5 39.59 ? PA ADP 402 A 1 HETATM 6 O O1A ADP . B . C 3 81.358 61.73 86.569 0.5 44.44 ? O1A ADP 402 A 1 HETATM 7 O O2A ADP . B . C 3 83.085 62.813 88.209 0.5 36.1 ? O2A ADP 402 A 1 HETATM 8 O O3A ADP . B . C 3 81.283 64.189 87.118 0.5 45.34 ? O3A ADP 402 A 1 HETATM 9 O O5' ADP . B . C 3 80.687 62.488 88.912 0.5 37.31 ? O5' ADP 402 A 1 HETATM 10 C C5' ADP . B . C 3 80.448 63.539 89.843 0.5 34.69 ? C5' ADP 402 A 1 HETATM 11 C C4' ADP . B . C 3 79.312 63.174 90.789 0.5 34.23 ? C4' ADP 402 A 1 HETATM 12 O O4' ADP . B . C 3 78.06 63.304 90.109 0.5 36.88 ? O4' ADP 402 A 1 HETATM 13 C C3' ADP . B . C 3 79.374 61.743 91.307 0.5 34.64 ? C3' ADP 402 A 1 HETATM 14 O O3' ADP . B . C 3 80.034 61.662 92.571 0.5 33.9 ? O3' ADP 402 A 1 HETATM 15 C C2' ADP . B . C 3 77.92 61.39 91.5 0.5 34.39 ? C2' ADP 402 A 1 HETATM 16 O O2' ADP . B . C 3 77.53 61.784 92.822 0.5 30.56 ? O2' ADP 402 A 1 HETATM 17 C C1' ADP . B . C 3 77.189 62.224 90.462 0.5 37.51 ? C1' ADP 402 A 1 HETATM 18 N N9 ADP . B . C 3 77.005 61.331 89.293 0.5 39.78 ? N9 ADP 402 A 1 HETATM 19 C C8 ADP . B . C 3 77.771 61.31 88.184 0.5 38.15 ? C8 ADP 402 A 1 HETATM 20 N N7 ADP . B . C 3 77.342 60.353 87.323 0.5 38.49 ? N7 ADP 402 A 1 HETATM 21 C C5 ADP . B . C 3 76.283 59.74 87.88 0.5 38.22 ? C5 ADP 402 A 1 HETATM 22 C C6 ADP . B . C 3 75.361 58.646 87.496 0.5 41.44 ? C6 ADP 402 A 1 HETATM 23 N N6 ADP . B . C 3 75.488 58 86.309 0.5 45.39 ? N6 ADP 402 A 1 HETATM 24 N N1 ADP . B . C 3 74.39 58.319 88.375 0.5 42.35 ? N1 ADP 402 A 1 HETATM 25 C C2 ADP . B . C 3 74.253 58.953 89.557 0.5 41.88 ? C2 ADP 402 A 1 HETATM 26 N N3 ADP . B . C 3 75.051 59.954 89.966 0.5 38.69 ? N3 ADP 402 A 1 HETATM 27 C C4 ADP . B . C 3 76.067 60.386 89.182 0.5 39.46 ? C4 ADP 402 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #