data_8Z55
#
_model_server_result.job_id            weEW82mqy34Eq5EYdqkBbQ 
_model_server_result.datetime_utc      '2024-10-16 12:28:08' 
_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          8z55 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    8Z55 
#
_exptl.entry_id    8Z55 
_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            8Z55 
_cell.length_a            46.198 
_cell.length_b            73.345 
_cell.length_c            163.938 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8Z55 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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
covale ? covale1 B C SER 6 B SER 121 1_555 B N SLL 7 B SLL 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale2 B C SLL 7 B SLL 122 1_555 B N GLN 8 B GLN 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
metalc ? metalc1 A SG CYS 138 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc2 A SG CYS 141 A CYS 169 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc3 A SG CYS 179 A CYS 207 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 
metalc ? metalc4 A SG CYS 184 A CYS 212 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
#
_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                     8Z55 
_atom_sites.fract_transf_matrix[1][1]    0.021646 
_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]    0.013634 
_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]    0.0061 
_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 1 401 303 ADP NAD . 
D 4 ZN A 1 402 401 ZN ZN . 
E 5 HOH A 1 501 136 HOH HOH . 
E 5 HOH A 2 502 128 HOH HOH . 
E 5 HOH A 3 503 98 HOH HOH . 
E 5 HOH A 4 504 29 HOH HOH . 
E 5 HOH A 5 505 133 HOH HOH . 
E 5 HOH A 6 506 27 HOH HOH . 
E 5 HOH A 7 507 63 HOH HOH . 
E 5 HOH A 8 508 101 HOH HOH . 
E 5 HOH A 9 509 135 HOH HOH . 
E 5 HOH A 10 510 40 HOH HOH . 
E 5 HOH A 11 511 144 HOH HOH . 
E 5 HOH A 12 512 39 HOH HOH . 
E 5 HOH A 13 513 120 HOH HOH . 
E 5 HOH A 14 514 119 HOH HOH . 
E 5 HOH A 15 515 36 HOH HOH . 
E 5 HOH A 16 516 34 HOH HOH . 
E 5 HOH A 17 517 8 HOH HOH . 
E 5 HOH A 18 518 146 HOH HOH . 
E 5 HOH A 19 519 107 HOH HOH . 
E 5 HOH A 20 520 117 HOH HOH . 
E 5 HOH A 21 521 86 HOH HOH . 
E 5 HOH A 22 522 7 HOH HOH . 
E 5 HOH A 23 523 67 HOH HOH . 
E 5 HOH A 24 524 24 HOH HOH . 
E 5 HOH A 25 525 100 HOH HOH . 
E 5 HOH A 26 526 2 HOH HOH . 
E 5 HOH A 27 527 147 HOH HOH . 
E 5 HOH A 28 528 65 HOH HOH . 
E 5 HOH A 29 529 5 HOH HOH . 
E 5 HOH A 30 530 104 HOH HOH . 
E 5 HOH A 31 531 3 HOH HOH . 
E 5 HOH A 32 532 76 HOH HOH . 
E 5 HOH A 33 533 142 HOH HOH . 
E 5 HOH A 34 534 71 HOH HOH . 
E 5 HOH A 35 535 13 HOH HOH . 
E 5 HOH A 36 536 17 HOH HOH . 
E 5 HOH A 37 537 61 HOH HOH . 
E 5 HOH A 38 538 88 HOH HOH . 
E 5 HOH A 39 539 42 HOH HOH . 
E 5 HOH A 40 540 154 HOH HOH . 
E 5 HOH A 41 541 4 HOH HOH . 
E 5 HOH A 42 542 14 HOH HOH . 
E 5 HOH A 43 543 96 HOH HOH . 
E 5 HOH A 44 544 49 HOH HOH . 
E 5 HOH A 45 545 138 HOH HOH . 
E 5 HOH A 46 546 111 HOH HOH . 
E 5 HOH A 47 547 35 HOH HOH . 
E 5 HOH A 48 548 116 HOH HOH . 
E 5 HOH A 49 549 58 HOH HOH . 
E 5 HOH A 50 550 18 HOH HOH . 
E 5 HOH A 51 551 102 HOH HOH . 
E 5 HOH A 52 552 137 HOH HOH . 
E 5 HOH A 53 553 90 HOH HOH . 
E 5 HOH A 54 554 20 HOH HOH . 
E 5 HOH A 55 555 72 HOH HOH . 
E 5 HOH A 56 556 148 HOH HOH . 
E 5 HOH A 57 557 69 HOH HOH . 
E 5 HOH A 58 558 79 HOH HOH . 
E 5 HOH A 59 559 80 HOH HOH . 
E 5 HOH A 60 560 37 HOH HOH . 
E 5 HOH A 61 561 126 HOH HOH . 
E 5 HOH A 62 562 9 HOH HOH . 
E 5 HOH A 63 563 66 HOH HOH . 
E 5 HOH A 64 564 57 HOH HOH . 
E 5 HOH A 65 565 73 HOH HOH . 
E 5 HOH A 66 566 1 HOH HOH . 
E 5 HOH A 67 567 89 HOH HOH . 
E 5 HOH A 68 568 52 HOH HOH . 
E 5 HOH A 69 569 97 HOH HOH . 
E 5 HOH A 70 570 16 HOH HOH . 
E 5 HOH A 71 571 33 HOH HOH . 
E 5 HOH A 72 572 127 HOH HOH . 
E 5 HOH A 73 573 84 HOH HOH . 
E 5 HOH A 74 574 48 HOH HOH . 
E 5 HOH A 75 575 15 HOH HOH . 
E 5 HOH A 76 576 25 HOH HOH . 
E 5 HOH A 77 577 139 HOH HOH . 
E 5 HOH A 78 578 59 HOH HOH . 
E 5 HOH A 79 579 103 HOH HOH . 
E 5 HOH A 80 580 21 HOH HOH . 
E 5 HOH A 81 581 31 HOH HOH . 
E 5 HOH A 82 582 47 HOH HOH . 
E 5 HOH A 83 583 30 HOH HOH . 
E 5 HOH A 84 584 19 HOH HOH . 
E 5 HOH A 85 585 92 HOH HOH . 
E 5 HOH A 86 586 26 HOH HOH . 
E 5 HOH A 87 587 74 HOH HOH . 
E 5 HOH A 88 588 105 HOH HOH . 
E 5 HOH A 89 589 62 HOH HOH . 
E 5 HOH A 90 590 70 HOH HOH . 
E 5 HOH A 91 591 41 HOH HOH . 
E 5 HOH A 92 592 23 HOH HOH . 
E 5 HOH A 93 593 46 HOH HOH . 
E 5 HOH A 94 594 51 HOH HOH . 
E 5 HOH A 95 595 99 HOH HOH . 
E 5 HOH A 96 596 45 HOH HOH . 
E 5 HOH A 97 597 6 HOH HOH . 
E 5 HOH A 98 598 83 HOH HOH . 
E 5 HOH A 99 599 68 HOH HOH . 
E 5 HOH A 100 600 115 HOH HOH . 
E 5 HOH A 101 601 140 HOH HOH . 
E 5 HOH A 102 602 114 HOH HOH . 
E 5 HOH A 103 603 10 HOH HOH . 
E 5 HOH A 104 604 38 HOH HOH . 
E 5 HOH A 105 605 44 HOH HOH . 
E 5 HOH A 106 606 155 HOH HOH . 
E 5 HOH A 107 607 106 HOH HOH . 
E 5 HOH A 108 608 82 HOH HOH . 
E 5 HOH A 109 609 125 HOH HOH . 
E 5 HOH A 110 610 32 HOH HOH . 
E 5 HOH A 111 611 87 HOH HOH . 
E 5 HOH A 112 612 78 HOH HOH . 
E 5 HOH A 113 613 53 HOH HOH . 
E 5 HOH A 114 614 11 HOH HOH . 
E 5 HOH A 115 615 55 HOH HOH . 
E 5 HOH A 116 616 22 HOH HOH . 
E 5 HOH A 117 617 153 HOH HOH . 
E 5 HOH A 118 618 50 HOH HOH . 
E 5 HOH A 119 619 132 HOH HOH . 
E 5 HOH A 120 620 130 HOH HOH . 
E 5 HOH A 121 621 94 HOH HOH . 
E 5 HOH A 122 622 54 HOH HOH . 
E 5 HOH A 123 623 149 HOH HOH . 
E 5 HOH A 124 624 131 HOH HOH . 
E 5 HOH A 125 625 77 HOH HOH . 
E 5 HOH A 126 626 43 HOH HOH . 
E 5 HOH A 127 627 110 HOH HOH . 
E 5 HOH A 128 628 95 HOH HOH . 
E 5 HOH A 129 629 143 HOH HOH . 
E 5 HOH A 130 630 129 HOH HOH . 
E 5 HOH A 131 631 64 HOH HOH . 
E 5 HOH A 132 632 109 HOH HOH . 
E 5 HOH A 133 633 75 HOH HOH . 
E 5 HOH A 134 634 91 HOH HOH . 
E 5 HOH A 135 635 85 HOH HOH . 
E 5 HOH A 136 636 141 HOH HOH . 
E 5 HOH A 137 637 56 HOH HOH . 
E 5 HOH A 138 638 113 HOH HOH . 
E 5 HOH A 139 639 28 HOH HOH . 
E 5 HOH A 140 640 124 HOH HOH . 
E 5 HOH A 141 641 108 HOH HOH . 
E 5 HOH A 142 642 81 HOH HOH . 
E 5 HOH A 143 643 12 HOH HOH . 
E 5 HOH A 144 644 145 HOH HOH . 
E 5 HOH A 145 645 152 HOH HOH . 
E 5 HOH A 146 646 123 HOH HOH . 
E 5 HOH A 147 647 112 HOH HOH . 
E 5 HOH A 148 648 121 HOH HOH . 
E 5 HOH A 149 649 134 HOH HOH . 
E 5 HOH A 150 650 122 HOH HOH . 
E 5 HOH A 151 651 150 HOH HOH . 
E 5 HOH A 152 652 60 HOH HOH . 
F 5 HOH B 1 301 93 HOH HOH . 
F 5 HOH B 2 302 151 HOH HOH . 
F 5 HOH B 3 303 118 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 30.035 -1.194 56.252 1 68.37 ? PB ADP 401 A 1 
HETATM 2 O O1B ADP . . . C 3 30.363 -0.467 55.004 1 67.18 ? O1B ADP 401 A 1 
HETATM 3 O O2B ADP . . . C 3 29.573 -0.431 57.432 1 65.22 ? O2B ADP 401 A 1 
HETATM 4 O O3B ADP . . . C 3 28.954 -2.349 55.935 1 67.39 ? O3B ADP 401 A 1 
HETATM 5 P PA ADP . . . C 3 32.287 -2.867 55.704 1 65.23 ? PA ADP 401 A 1 
HETATM 6 O O1A ADP . . . C 3 31.451 -3.615 54.742 1 59.97 ? O1A ADP 401 A 1 
HETATM 7 O O2A ADP . . . C 3 33.317 -3.591 56.493 1 62.01 ? O2A ADP 401 A 1 
HETATM 8 O O3A ADP . . . C 3 31.326 -2.056 56.724 1 69.39 ? O3A ADP 401 A 1 
HETATM 9 O O5' ADP . . . C 3 33.015 -1.644 54.915 1 61.53 ? O5' ADP 401 A 1 
HETATM 10 C C5' ADP . . . C 3 34.194 -0.979 55.401 1 52.79 ? C5' ADP 401 A 1 
HETATM 11 C C4' ADP . . . C 3 34.483 0.219 54.482 1 48.99 ? C4' ADP 401 A 1 
HETATM 12 O O4' ADP . . . C 3 35.247 1.185 55.259 1 45.09 ? O4' ADP 401 A 1 
HETATM 13 C C3' ADP . . . C 3 35.395 -0.148 53.3 1 41.95 ? C3' ADP 401 A 1 
HETATM 14 O O3' ADP . . . C 3 35.13 0.744 52.231 1 39.45 ? O3' ADP 401 A 1 
HETATM 15 C C2' ADP . . . C 3 36.749 0.188 53.878 1 38.5 ? C2' ADP 401 A 1 
HETATM 16 O O2' ADP . . . C 3 37.741 0.377 52.835 1 38.83 ? O2' ADP 401 A 1 
HETATM 17 C C1' ADP . . . C 3 36.407 1.512 54.49 1 46.3 ? C1' ADP 401 A 1 
HETATM 18 N N9 ADP . . . C 3 37.402 1.921 55.507 1 53.73 ? N9 ADP 401 A 1 
HETATM 19 C C8 ADP . . . C 3 38.137 1.084 56.24 1 56.58 ? C8 ADP 401 A 1 
HETATM 20 N N7 ADP . . . C 3 38.895 1.806 57.064 1 55.85 ? N7 ADP 401 A 1 
HETATM 21 C C5 ADP . . . C 3 38.616 3.092 56.847 1 56.44 ? C5 ADP 401 A 1 
HETATM 22 C C6 ADP . . . C 3 39.096 4.199 57.41 1 60.45 ? C6 ADP 401 A 1 
HETATM 23 N N6 ADP . . . C 3 40.023 4.012 58.344 1 58.29 ? N6 ADP 401 A 1 
HETATM 24 N N1 ADP . . . C 3 38.675 5.424 57.051 1 57.27 ? N1 ADP 401 A 1 
HETATM 25 C C2 ADP . . . C 3 37.705 5.535 56.048 1 52.77 ? C2 ADP 401 A 1 
HETATM 26 N N3 ADP . . . C 3 37.215 4.353 55.473 1 51.22 ? N3 ADP 401 A 1 
HETATM 27 C C4 ADP . . . C 3 37.685 3.164 55.89 1 53.98 ? C4 ADP 401 A 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#