data_4E1D # _model_server_result.job_id owAYILRbrYwyar7W6KqQEA _model_server_result.datetime_utc '2025-03-25 20:06:09' _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 4e1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4E1D # _exptl.entry_id 4E1D _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 4E1D _cell.length_a 128.39 _cell.length_b 128.39 _cell.length_c 76.72 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4E1D _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 2 2' # _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 _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 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 A OE2 GLU 28 A GLU 16 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc2 A OE2 GLU 28 A GLU 16 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc3 A OE1 GLU 90 A GLU 78 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc4 A OE1 GLN 174 A GLN 162 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc5 B O3B ADP . A ADP 401 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc6 B O2A ADP . A ADP 401 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc7 D MN MN . A MN 403 1_555 H O HOH . A HOH 636 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? # _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 4E1D _atom_sites.fract_transf_matrix[1][1] 0.007789 _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] 0.007789 _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] 0.013034 _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 1 401 401 ADP ADP . C 3 MN A 1 402 402 MN MN . D 3 MN A 1 403 403 MN MN . E 4 SO4 A 1 404 404 SO4 SO4 . F 4 SO4 A 1 405 405 SO4 SO4 . G 4 SO4 A 1 406 406 SO4 SO4 . H 5 HOH A 1 501 501 HOH HOH . H 5 HOH A 2 502 502 HOH HOH . H 5 HOH A 3 503 503 HOH HOH . H 5 HOH A 4 504 504 HOH HOH . H 5 HOH A 5 505 505 HOH HOH . H 5 HOH A 6 506 506 HOH HOH . H 5 HOH A 7 507 507 HOH HOH . H 5 HOH A 8 508 508 HOH HOH . H 5 HOH A 9 509 509 HOH HOH . H 5 HOH A 10 510 510 HOH HOH . H 5 HOH A 11 511 511 HOH HOH . H 5 HOH A 12 512 512 HOH HOH . H 5 HOH A 13 513 513 HOH HOH . H 5 HOH A 14 514 514 HOH HOH . H 5 HOH A 15 515 515 HOH HOH . H 5 HOH A 16 516 516 HOH HOH . H 5 HOH A 17 517 517 HOH HOH . H 5 HOH A 18 518 518 HOH HOH . H 5 HOH A 19 519 519 HOH HOH . H 5 HOH A 20 520 520 HOH HOH . H 5 HOH A 21 521 521 HOH HOH . H 5 HOH A 22 522 522 HOH HOH . H 5 HOH A 23 523 523 HOH HOH . H 5 HOH A 24 524 524 HOH HOH . H 5 HOH A 25 525 525 HOH HOH . H 5 HOH A 26 526 526 HOH HOH . H 5 HOH A 27 527 527 HOH HOH . H 5 HOH A 28 528 528 HOH HOH . H 5 HOH A 29 529 529 HOH HOH . H 5 HOH A 30 530 530 HOH HOH . H 5 HOH A 31 531 531 HOH HOH . H 5 HOH A 32 532 532 HOH HOH . H 5 HOH A 33 533 533 HOH HOH . H 5 HOH A 34 534 534 HOH HOH . H 5 HOH A 35 535 535 HOH HOH . H 5 HOH A 36 536 536 HOH HOH . H 5 HOH A 37 537 537 HOH HOH . H 5 HOH A 38 538 538 HOH HOH . H 5 HOH A 39 539 540 HOH HOH . H 5 HOH A 40 540 541 HOH HOH . H 5 HOH A 41 541 542 HOH HOH . H 5 HOH A 42 542 543 HOH HOH . H 5 HOH A 43 543 544 HOH HOH . H 5 HOH A 44 544 545 HOH HOH . H 5 HOH A 45 545 546 HOH HOH . H 5 HOH A 46 546 547 HOH HOH . H 5 HOH A 47 547 548 HOH HOH . H 5 HOH A 48 548 549 HOH HOH . H 5 HOH A 49 549 550 HOH HOH . H 5 HOH A 50 550 551 HOH HOH . H 5 HOH A 51 551 552 HOH HOH . H 5 HOH A 52 552 553 HOH HOH . H 5 HOH A 53 553 554 HOH HOH . H 5 HOH A 54 554 555 HOH HOH . H 5 HOH A 55 555 556 HOH HOH . H 5 HOH A 56 556 557 HOH HOH . H 5 HOH A 57 557 558 HOH HOH . H 5 HOH A 58 558 559 HOH HOH . H 5 HOH A 59 559 560 HOH HOH . H 5 HOH A 60 560 561 HOH HOH . H 5 HOH A 61 561 562 HOH HOH . H 5 HOH A 62 562 563 HOH HOH . H 5 HOH A 63 563 564 HOH HOH . H 5 HOH A 64 564 565 HOH HOH . H 5 HOH A 65 565 567 HOH HOH . H 5 HOH A 66 566 568 HOH HOH . H 5 HOH A 67 567 570 HOH HOH . H 5 HOH A 68 568 572 HOH HOH . H 5 HOH A 69 569 573 HOH HOH . H 5 HOH A 70 570 574 HOH HOH . H 5 HOH A 71 571 575 HOH HOH . H 5 HOH A 72 572 576 HOH HOH . H 5 HOH A 73 573 578 HOH HOH . H 5 HOH A 74 574 579 HOH HOH . H 5 HOH A 75 575 580 HOH HOH . H 5 HOH A 76 576 581 HOH HOH . H 5 HOH A 77 577 582 HOH HOH . H 5 HOH A 78 578 583 HOH HOH . H 5 HOH A 79 579 584 HOH HOH . H 5 HOH A 80 580 585 HOH HOH . H 5 HOH A 81 581 586 HOH HOH . H 5 HOH A 82 582 588 HOH HOH . H 5 HOH A 83 583 589 HOH HOH . H 5 HOH A 84 584 590 HOH HOH . H 5 HOH A 85 585 592 HOH HOH . H 5 HOH A 86 586 593 HOH HOH . H 5 HOH A 87 587 594 HOH HOH . H 5 HOH A 88 588 595 HOH HOH . H 5 HOH A 89 589 596 HOH HOH . H 5 HOH A 90 590 597 HOH HOH . H 5 HOH A 91 591 598 HOH HOH . H 5 HOH A 92 592 599 HOH HOH . H 5 HOH A 93 593 600 HOH HOH . H 5 HOH A 94 594 601 HOH HOH . H 5 HOH A 95 595 602 HOH HOH . H 5 HOH A 96 596 603 HOH HOH . H 5 HOH A 97 597 604 HOH HOH . H 5 HOH A 98 598 605 HOH HOH . H 5 HOH A 99 599 606 HOH HOH . H 5 HOH A 100 600 608 HOH HOH . H 5 HOH A 101 601 609 HOH HOH . H 5 HOH A 102 602 610 HOH HOH . H 5 HOH A 103 603 613 HOH HOH . H 5 HOH A 104 604 615 HOH HOH . H 5 HOH A 105 605 616 HOH HOH . H 5 HOH A 106 606 617 HOH HOH . H 5 HOH A 107 607 619 HOH HOH . H 5 HOH A 108 608 620 HOH HOH . H 5 HOH A 109 609 621 HOH HOH . H 5 HOH A 110 610 622 HOH HOH . H 5 HOH A 111 611 623 HOH HOH . H 5 HOH A 112 612 624 HOH HOH . H 5 HOH A 113 613 625 HOH HOH . H 5 HOH A 114 614 626 HOH HOH . H 5 HOH A 115 615 627 HOH HOH . H 5 HOH A 116 616 629 HOH HOH . H 5 HOH A 117 617 631 HOH HOH . H 5 HOH A 118 618 632 HOH HOH . H 5 HOH A 119 619 633 HOH HOH . H 5 HOH A 120 620 634 HOH HOH . H 5 HOH A 121 621 638 HOH HOH . H 5 HOH A 122 622 639 HOH HOH . H 5 HOH A 123 623 640 HOH HOH . H 5 HOH A 124 624 641 HOH HOH . H 5 HOH A 125 625 642 HOH HOH . H 5 HOH A 126 626 643 HOH HOH . H 5 HOH A 127 627 645 HOH HOH . H 5 HOH A 128 628 646 HOH HOH . H 5 HOH A 129 629 647 HOH HOH . H 5 HOH A 130 630 648 HOH HOH . H 5 HOH A 131 631 649 HOH HOH . H 5 HOH A 132 632 650 HOH HOH . H 5 HOH A 133 633 651 HOH HOH . H 5 HOH A 134 634 652 HOH HOH . H 5 HOH A 135 635 653 HOH HOH . H 5 HOH A 136 636 655 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 34.017 87.577 4.112 1 52.96 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 34.963 86.744 3.36 1 48.27 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 32.598 87.027 3.95 1 56.1 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 34.073 89.017 3.621 1 54.35 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 35.731 87.742 6.534 1 52.37 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 36.208 86.463 7.115 1 58.11 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 36.848 88.347 5.639 1 52.23 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 34.404 87.51 5.665 1 57.25 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 35.383 88.768 7.702 1 43.83 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 34.196 88.522 8.47 1 34.77 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 33.822 89.763 9.237 1 27.9 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 32.884 89.429 10.283 1 28.73 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 34.966 90.517 9.913 1 24.39 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 34.859 91.925 9.729 1 20.1 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 34.867 90.055 11.369 1 28.37 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 35.356 90.996 12.314 1 28.94 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 33.364 89.912 11.521 1 30.52 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 32.931 89 12.583 1 30.64 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 33.342 87.713 12.791 1 31.26 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 32.8 87.149 13.848 1 31.99 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 31.971 88.139 14.363 1 33.56 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 31.144 88.192 15.501 1 35.87 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 31.05 87.208 16.385 1 38.49 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 30.468 89.344 15.734 1 32.65 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 30.628 90.369 14.883 1 29.53 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 31.391 90.442 13.787 1 27.63 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 32.044 89.288 13.577 1 30.37 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #