data_6LZI # _model_server_result.job_id WXIXCgUEHfMiGYJUvCvciA _model_server_result.datetime_utc '2024-10-20 03:43:17' _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 6lzi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":407}' # _entry.id 6LZI # _exptl.entry_id 6LZI _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 80.978 _cell.angle_beta 71.521 _cell.angle_gamma 77.707 _cell.entry_id 6LZI _cell.length_a 35.017 _cell.length_b 42.906 _cell.length_c 53.845 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LZI _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # _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 _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 4 _struct_asym.id H _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 26 A ASN 26 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc2 B MG MG . A MG 401 1_555 H O1B ADP . A ADP 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc3 B MG MG . A MG 401 1_555 H O2A ADP . A ADP 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc4 B MG MG . A MG 401 1_555 I O HOH . A HOH 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc5 B MG MG . A MG 401 1_555 I O HOH . A HOH 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc6 B MG MG . A MG 401 1_555 I O HOH . A HOH 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? # _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 6LZI _atom_sites.fract_transf_matrix[1][1] 0.028558 _atom_sites.fract_transf_matrix[1][2] -0.006223 _atom_sites.fract_transf_matrix[1][3] -0.008986 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023854 _atom_sites.fract_transf_matrix[2][3] -0.00231 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.019673 _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 MG A 1 401 1 MG MG . C 3 PEG A 1 402 4 PEG PEG . D 3 PEG A 1 403 5 PEG PEG . E 3 PEG A 1 404 6 PEG PEG . F 3 PEG A 1 405 7 PEG PEG . G 3 PEG A 1 406 8 PEG PEG . H 4 ADP A 1 407 1 ADP ADP . I 5 HOH A 1 501 133 HOH HOH . I 5 HOH A 2 502 112 HOH HOH . I 5 HOH A 3 503 115 HOH HOH . I 5 HOH A 4 504 135 HOH HOH . I 5 HOH A 5 505 174 HOH HOH . I 5 HOH A 6 506 185 HOH HOH . I 5 HOH A 7 507 146 HOH HOH . I 5 HOH A 8 508 172 HOH HOH . I 5 HOH A 9 509 153 HOH HOH . I 5 HOH A 10 510 61 HOH HOH . I 5 HOH A 11 511 43 HOH HOH . I 5 HOH A 12 512 145 HOH HOH . I 5 HOH A 13 513 34 HOH HOH . I 5 HOH A 14 514 64 HOH HOH . I 5 HOH A 15 515 50 HOH HOH . I 5 HOH A 16 516 198 HOH HOH . I 5 HOH A 17 517 62 HOH HOH . I 5 HOH A 18 518 170 HOH HOH . I 5 HOH A 19 519 45 HOH HOH . I 5 HOH A 20 520 55 HOH HOH . I 5 HOH A 21 521 7 HOH HOH . I 5 HOH A 22 522 77 HOH HOH . I 5 HOH A 23 523 192 HOH HOH . I 5 HOH A 24 524 80 HOH HOH . I 5 HOH A 25 525 31 HOH HOH . I 5 HOH A 26 526 49 HOH HOH . I 5 HOH A 27 527 14 HOH HOH . I 5 HOH A 28 528 123 HOH HOH . I 5 HOH A 29 529 69 HOH HOH . I 5 HOH A 30 530 68 HOH HOH . I 5 HOH A 31 531 9 HOH HOH . I 5 HOH A 32 532 13 HOH HOH . I 5 HOH A 33 533 87 HOH HOH . I 5 HOH A 34 534 25 HOH HOH . I 5 HOH A 35 535 21 HOH HOH . I 5 HOH A 36 536 105 HOH HOH . I 5 HOH A 37 537 178 HOH HOH . I 5 HOH A 38 538 78 HOH HOH . I 5 HOH A 39 539 24 HOH HOH . I 5 HOH A 40 540 23 HOH HOH . I 5 HOH A 41 541 57 HOH HOH . I 5 HOH A 42 542 39 HOH HOH . I 5 HOH A 43 543 19 HOH HOH . I 5 HOH A 44 544 175 HOH HOH . I 5 HOH A 45 545 28 HOH HOH . I 5 HOH A 46 546 18 HOH HOH . I 5 HOH A 47 547 17 HOH HOH . I 5 HOH A 48 548 202 HOH HOH . I 5 HOH A 49 549 195 HOH HOH . I 5 HOH A 50 550 52 HOH HOH . I 5 HOH A 51 551 1 HOH HOH . I 5 HOH A 52 552 2 HOH HOH . I 5 HOH A 53 553 73 HOH HOH . I 5 HOH A 54 554 44 HOH HOH . I 5 HOH A 55 555 15 HOH HOH . I 5 HOH A 56 556 96 HOH HOH . I 5 HOH A 57 557 193 HOH HOH . I 5 HOH A 58 558 74 HOH HOH . I 5 HOH A 59 559 5 HOH HOH . I 5 HOH A 60 560 79 HOH HOH . I 5 HOH A 61 561 88 HOH HOH . I 5 HOH A 62 562 136 HOH HOH . I 5 HOH A 63 563 3 HOH HOH . I 5 HOH A 64 564 83 HOH HOH . I 5 HOH A 65 565 26 HOH HOH . I 5 HOH A 66 566 58 HOH HOH . I 5 HOH A 67 567 11 HOH HOH . I 5 HOH A 68 568 150 HOH HOH . I 5 HOH A 69 569 188 HOH HOH . I 5 HOH A 70 570 194 HOH HOH . I 5 HOH A 71 571 6 HOH HOH . I 5 HOH A 72 572 8 HOH HOH . I 5 HOH A 73 573 30 HOH HOH . I 5 HOH A 74 574 125 HOH HOH . I 5 HOH A 75 575 196 HOH HOH . I 5 HOH A 76 576 113 HOH HOH . I 5 HOH A 77 577 152 HOH HOH . I 5 HOH A 78 578 47 HOH HOH . I 5 HOH A 79 579 35 HOH HOH . I 5 HOH A 80 580 48 HOH HOH . I 5 HOH A 81 581 41 HOH HOH . I 5 HOH A 82 582 66 HOH HOH . I 5 HOH A 83 583 59 HOH HOH . I 5 HOH A 84 584 191 HOH HOH . I 5 HOH A 85 585 29 HOH HOH . I 5 HOH A 86 586 161 HOH HOH . I 5 HOH A 87 587 120 HOH HOH . I 5 HOH A 88 588 201 HOH HOH . I 5 HOH A 89 589 187 HOH HOH . I 5 HOH A 90 590 184 HOH HOH . I 5 HOH A 91 591 37 HOH HOH . I 5 HOH A 92 592 104 HOH HOH . I 5 HOH A 93 593 22 HOH HOH . I 5 HOH A 94 594 16 HOH HOH . I 5 HOH A 95 595 81 HOH HOH . I 5 HOH A 96 596 63 HOH HOH . I 5 HOH A 97 597 140 HOH HOH . I 5 HOH A 98 598 117 HOH HOH . I 5 HOH A 99 599 56 HOH HOH . I 5 HOH A 100 600 4 HOH HOH . I 5 HOH A 101 601 124 HOH HOH . I 5 HOH A 102 602 38 HOH HOH . I 5 HOH A 103 603 197 HOH HOH . I 5 HOH A 104 604 139 HOH HOH . I 5 HOH A 105 605 163 HOH HOH . I 5 HOH A 106 606 20 HOH HOH . I 5 HOH A 107 607 70 HOH HOH . I 5 HOH A 108 608 10 HOH HOH . I 5 HOH A 109 609 128 HOH HOH . I 5 HOH A 110 610 95 HOH HOH . I 5 HOH A 111 611 82 HOH HOH . I 5 HOH A 112 612 51 HOH HOH . I 5 HOH A 113 613 33 HOH HOH . I 5 HOH A 114 614 32 HOH HOH . I 5 HOH A 115 615 151 HOH HOH . I 5 HOH A 116 616 60 HOH HOH . I 5 HOH A 117 617 40 HOH HOH . I 5 HOH A 118 618 156 HOH HOH . I 5 HOH A 119 619 126 HOH HOH . I 5 HOH A 120 620 110 HOH HOH . I 5 HOH A 121 621 91 HOH HOH . I 5 HOH A 122 622 89 HOH HOH . I 5 HOH A 123 623 147 HOH HOH . I 5 HOH A 124 624 143 HOH HOH . I 5 HOH A 125 625 182 HOH HOH . I 5 HOH A 126 626 137 HOH HOH . I 5 HOH A 127 627 164 HOH HOH . I 5 HOH A 128 628 186 HOH HOH . I 5 HOH A 129 629 168 HOH HOH . I 5 HOH A 130 630 46 HOH HOH . I 5 HOH A 131 631 176 HOH HOH . I 5 HOH A 132 632 92 HOH HOH . I 5 HOH A 133 633 199 HOH HOH . I 5 HOH A 134 634 118 HOH HOH . I 5 HOH A 135 635 200 HOH HOH . I 5 HOH A 136 636 101 HOH HOH . I 5 HOH A 137 637 67 HOH HOH . I 5 HOH A 138 638 177 HOH HOH . I 5 HOH A 139 639 86 HOH HOH . I 5 HOH A 140 640 165 HOH HOH . I 5 HOH A 141 641 144 HOH HOH . I 5 HOH A 142 642 71 HOH HOH . I 5 HOH A 143 643 154 HOH HOH . I 5 HOH A 144 644 84 HOH HOH . I 5 HOH A 145 645 141 HOH HOH . I 5 HOH A 146 646 109 HOH HOH . I 5 HOH A 147 647 75 HOH HOH . I 5 HOH A 148 648 148 HOH HOH . I 5 HOH A 149 649 167 HOH HOH . I 5 HOH A 150 650 98 HOH HOH . I 5 HOH A 151 651 72 HOH HOH . I 5 HOH A 152 652 76 HOH HOH . I 5 HOH A 153 653 108 HOH HOH . I 5 HOH A 154 654 159 HOH HOH . I 5 HOH A 155 655 36 HOH HOH . I 5 HOH A 156 656 114 HOH HOH . I 5 HOH A 157 657 97 HOH HOH . I 5 HOH A 158 658 138 HOH HOH . I 5 HOH A 159 659 99 HOH HOH . I 5 HOH A 160 660 54 HOH HOH . I 5 HOH A 161 661 157 HOH HOH . I 5 HOH A 162 662 160 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 . . . H 4 7.305 38.536 -28.297 1 32.34 ? PB ADP 407 A 1 HETATM 2 O O1B ADP . . . H 4 7.796 37.192 -28.717 1 26.41 ? O1B ADP 407 A 1 HETATM 3 O O2B ADP . . . H 4 5.829 38.775 -28.711 1 33.18 ? O2B ADP 407 A 1 HETATM 4 O O3B ADP . . . H 4 7.49 38.771 -26.814 1 35.93 ? O3B ADP 407 A 1 HETATM 5 P PA ADP . . . H 4 9.27 39.304 -30.237 1 29.16 ? PA ADP 407 A 1 HETATM 6 O O1A ADP . . . H 4 9.878 40.625 -30.61 1 27.95 ? O1A ADP 407 A 1 HETATM 7 O O2A ADP . . . H 4 10.241 38.258 -29.807 1 21.34 ? O2A ADP 407 A 1 HETATM 8 O O3A ADP . . . H 4 8.159 39.651 -29.058 1 31.48 ? O3A ADP 407 A 1 HETATM 9 O O5' ADP . . . H 4 8.535 38.649 -31.518 1 29.56 ? O5' ADP 407 A 1 HETATM 10 C C5' ADP . . . H 4 7.453 39.481 -31.94 1 33.5 ? C5' ADP 407 A 1 HETATM 11 C C4' ADP . . . H 4 6.385 38.651 -32.646 1 34.04 ? C4' ADP 407 A 1 HETATM 12 O O4' ADP . . . H 4 6.909 38.166 -33.858 1 30.9 ? O4' ADP 407 A 1 HETATM 13 C C3' ADP . . . H 4 5.874 37.43 -31.909 1 28.51 ? C3' ADP 407 A 1 HETATM 14 O O3' ADP . . . H 4 4.728 37.799 -31.095 1 33.17 ? O3' ADP 407 A 1 HETATM 15 C C2' ADP . . . H 4 5.414 36.534 -33.044 1 26.31 ? C2' ADP 407 A 1 HETATM 16 O O2' ADP . . . H 4 4.085 37.048 -33.385 1 30.85 ? O2' ADP 407 A 1 HETATM 17 C C1' ADP . . . H 4 6.341 36.91 -34.173 1 24.26 ? C1' ADP 407 A 1 HETATM 18 N N9 ADP . . . H 4 7.462 35.988 -34.313 1 23.12 ? N9 ADP 407 A 1 HETATM 19 C C8 ADP . . . H 4 8.763 36.196 -33.973 1 22.37 ? C8 ADP 407 A 1 HETATM 20 N N7 ADP . . . H 4 9.526 35.113 -34.278 1 20.33 ? N7 ADP 407 A 1 HETATM 21 C C5 ADP . . . H 4 8.655 34.208 -34.796 1 21.65 ? C5 ADP 407 A 1 HETATM 22 C C6 ADP . . . H 4 8.83 32.847 -35.31 1 20.71 ? C6 ADP 407 A 1 HETATM 23 N N6 ADP . . . H 4 10.059 32.262 -35.284 1 22.42 ? N6 ADP 407 A 1 HETATM 24 N N1 ADP . . . H 4 7.721 32.208 -35.773 1 21.97 ? N1 ADP 407 A 1 HETATM 25 C C2 ADP . . . H 4 6.479 32.847 -35.736 1 20.06 ? C2 ADP 407 A 1 HETATM 26 N N3 ADP . . . H 4 6.257 34.087 -35.306 1 22.08 ? N3 ADP 407 A 1 HETATM 27 C C4 ADP . . . H 4 7.332 34.784 -34.849 1 23.93 ? C4 ADP 407 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #