data_1NB9
#
_model_server_result.job_id            ZbAcXJ9TDEE6o0vM1Ix1cA 
_model_server_result.datetime_utc      '2025-03-09 03:42:53' 
_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          1nb9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    1NB9 
#
_exptl.entry_id    1NB9 
_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            1NB9 
_cell.length_a            56.957 
_cell.length_b            56.957 
_cell.length_c            82.501 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1NB9 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_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 
#
_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
metalc ? metalc1 A O THR 26 A THR 34 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc2 A OG1 THR 26 A THR 34 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc3 B MG MG . A MG 201 1_555 C O1B ADP . A ADP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc4 B MG MG . A MG 201 1_555 C O2A ADP . A ADP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc5 B MG MG . A MG 201 1_555 E O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
metalc ? metalc6 B MG MG . A MG 201 1_555 E O HOH . A HOH 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
#
_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                     1NB9 
_atom_sites.fract_transf_matrix[1][1]    0.017557 
_atom_sites.fract_transf_matrix[1][2]    0.010137 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020273 
_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]    0.012121 
_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 1 201 301 MG MG . 
C 3 ADP A 1 301 201 ADP ADP . 
D 4 RBF A 1 401 401 RBF RBF . 
E 5 HOH A 1 501 501 HOH HOH . 
E 5 HOH A 2 502 502 HOH HOH . 
E 5 HOH A 3 503 503 HOH HOH . 
E 5 HOH A 4 504 504 HOH HOH . 
E 5 HOH A 5 505 505 HOH HOH . 
E 5 HOH A 6 506 506 HOH HOH . 
E 5 HOH A 7 507 507 HOH HOH . 
E 5 HOH A 8 508 508 HOH HOH . 
E 5 HOH A 9 509 509 HOH HOH . 
E 5 HOH A 10 510 510 HOH HOH . 
E 5 HOH A 11 511 511 HOH HOH . 
E 5 HOH A 12 512 512 HOH HOH . 
E 5 HOH A 13 513 513 HOH HOH . 
E 5 HOH A 14 514 514 HOH HOH . 
E 5 HOH A 15 515 515 HOH HOH . 
E 5 HOH A 16 516 516 HOH HOH . 
E 5 HOH A 17 517 517 HOH HOH . 
E 5 HOH A 18 518 518 HOH HOH . 
E 5 HOH A 19 519 519 HOH HOH . 
E 5 HOH A 20 520 520 HOH HOH . 
E 5 HOH A 21 521 521 HOH HOH . 
E 5 HOH A 22 522 522 HOH HOH . 
E 5 HOH A 23 523 523 HOH HOH . 
E 5 HOH A 24 524 524 HOH HOH . 
E 5 HOH A 25 525 525 HOH HOH . 
E 5 HOH A 26 526 526 HOH HOH . 
E 5 HOH A 27 527 527 HOH HOH . 
E 5 HOH A 28 528 528 HOH HOH . 
E 5 HOH A 29 529 529 HOH HOH . 
E 5 HOH A 30 530 530 HOH HOH . 
E 5 HOH A 31 531 531 HOH HOH . 
E 5 HOH A 32 532 532 HOH HOH . 
E 5 HOH A 33 533 533 HOH HOH . 
E 5 HOH A 34 534 534 HOH HOH . 
E 5 HOH A 35 535 535 HOH HOH . 
E 5 HOH A 36 536 536 HOH HOH . 
E 5 HOH A 37 537 537 HOH HOH . 
E 5 HOH A 38 538 538 HOH HOH . 
E 5 HOH A 39 539 539 HOH HOH . 
E 5 HOH A 40 540 540 HOH HOH . 
E 5 HOH A 41 541 541 HOH HOH . 
E 5 HOH A 42 542 542 HOH HOH . 
E 5 HOH A 43 543 543 HOH HOH . 
E 5 HOH A 44 544 544 HOH HOH . 
E 5 HOH A 45 545 545 HOH HOH . 
E 5 HOH A 46 546 546 HOH HOH . 
E 5 HOH A 47 547 547 HOH HOH . 
E 5 HOH A 48 548 548 HOH HOH . 
E 5 HOH A 49 549 549 HOH HOH . 
E 5 HOH A 50 550 550 HOH HOH . 
E 5 HOH A 51 551 551 HOH HOH . 
E 5 HOH A 52 552 552 HOH HOH . 
E 5 HOH A 53 553 553 HOH HOH . 
E 5 HOH A 54 554 554 HOH HOH . 
E 5 HOH A 55 555 555 HOH HOH . 
E 5 HOH A 56 556 556 HOH HOH . 
E 5 HOH A 57 557 557 HOH HOH . 
E 5 HOH A 58 558 558 HOH HOH . 
E 5 HOH A 59 559 559 HOH HOH . 
E 5 HOH A 60 560 560 HOH HOH . 
E 5 HOH A 61 561 561 HOH HOH . 
E 5 HOH A 62 562 562 HOH HOH . 
E 5 HOH A 63 563 563 HOH HOH . 
E 5 HOH A 64 564 564 HOH HOH . 
E 5 HOH A 65 565 565 HOH HOH . 
E 5 HOH A 66 566 566 HOH HOH . 
E 5 HOH A 67 567 567 HOH HOH . 
E 5 HOH A 68 568 568 HOH HOH . 
E 5 HOH A 69 569 569 HOH HOH . 
E 5 HOH A 70 570 570 HOH HOH . 
E 5 HOH A 71 571 571 HOH HOH . 
E 5 HOH A 72 572 572 HOH HOH . 
E 5 HOH A 73 573 573 HOH HOH . 
E 5 HOH A 74 574 574 HOH HOH . 
E 5 HOH A 75 575 575 HOH HOH . 
E 5 HOH A 76 576 576 HOH HOH . 
E 5 HOH A 77 577 577 HOH HOH . 
E 5 HOH A 78 578 578 HOH HOH . 
E 5 HOH A 79 579 579 HOH HOH . 
E 5 HOH A 80 580 580 HOH HOH . 
E 5 HOH A 81 581 581 HOH HOH . 
E 5 HOH A 82 582 582 HOH HOH . 
E 5 HOH A 83 583 583 HOH HOH . 
E 5 HOH A 84 584 584 HOH HOH . 
E 5 HOH A 85 585 585 HOH HOH . 
E 5 HOH A 86 586 586 HOH HOH . 
E 5 HOH A 87 587 587 HOH HOH . 
E 5 HOH A 88 588 588 HOH HOH . 
E 5 HOH A 89 589 589 HOH HOH . 
E 5 HOH A 90 590 590 HOH HOH . 
E 5 HOH A 91 591 591 HOH HOH . 
E 5 HOH A 92 592 592 HOH HOH . 
E 5 HOH A 93 593 593 HOH HOH . 
E 5 HOH A 94 594 594 HOH HOH . 
E 5 HOH A 95 595 595 HOH HOH . 
E 5 HOH A 96 596 596 HOH HOH . 
E 5 HOH A 97 597 597 HOH HOH . 
E 5 HOH A 98 598 598 HOH HOH . 
E 5 HOH A 99 599 599 HOH HOH . 
E 5 HOH A 100 600 600 HOH HOH . 
E 5 HOH A 101 601 601 HOH HOH . 
E 5 HOH A 102 602 602 HOH HOH . 
E 5 HOH A 103 603 603 HOH HOH . 
E 5 HOH A 104 604 604 HOH HOH . 
E 5 HOH A 105 605 605 HOH HOH . 
E 5 HOH A 106 606 606 HOH HOH . 
E 5 HOH A 107 607 607 HOH HOH . 
E 5 HOH A 108 608 608 HOH HOH . 
E 5 HOH A 109 609 609 HOH HOH . 
E 5 HOH A 110 610 610 HOH HOH . 
E 5 HOH A 111 611 611 HOH HOH . 
E 5 HOH A 112 612 612 HOH HOH . 
E 5 HOH A 113 613 613 HOH HOH . 
E 5 HOH A 114 614 614 HOH HOH . 
E 5 HOH A 115 615 615 HOH HOH . 
E 5 HOH A 116 616 616 HOH HOH . 
E 5 HOH A 117 617 617 HOH HOH . 
E 5 HOH A 118 618 618 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 -1.941 27.686 22.233 1 20.28 ? PB ADP 301 A 1 
HETATM 2 O O1B ADP . . . C 3 -2.326 28.218 23.561 1 19.51 ? O1B ADP 301 A 1 
HETATM 3 O O2B ADP . . . C 3 -2.8 26.525 21.734 1 20.22 ? O2B ADP 301 A 1 
HETATM 4 O O3B ADP . . . C 3 -1.93 28.822 21.269 1 21.75 ? O3B ADP 301 A 1 
HETATM 5 P PA ADP . . . C 3 0.469 26.463 23.374 1 19.34 ? PA ADP 301 A 1 
HETATM 6 O O1A ADP . . . C 3 1.924 26.804 23.009 1 19.76 ? O1A ADP 301 A 1 
HETATM 7 O O2A ADP . . . C 3 0.026 26.891 24.778 1 19.05 ? O2A ADP 301 A 1 
HETATM 8 O O3A ADP . . . C 3 -0.405 27.183 22.282 1 19.22 ? O3A ADP 301 A 1 
HETATM 9 O O5' ADP . . . C 3 0.322 24.93 23.219 1 18.2 ? O5' ADP 301 A 1 
HETATM 10 C C5' ADP . . . C 3 -0.95 24.313 23.542 1 19.69 ? C5' ADP 301 A 1 
HETATM 11 C C4' ADP . . . C 3 -1.153 22.983 22.819 1 20.46 ? C4' ADP 301 A 1 
HETATM 12 O O4' ADP . . . C 3 -0.198 22.025 23.212 1 20.39 ? O4' ADP 301 A 1 
HETATM 13 C C3' ADP . . . C 3 -2.464 22.249 23.136 1 20.04 ? C3' ADP 301 A 1 
HETATM 14 O O3' ADP . . . C 3 -3.569 22.664 22.324 1 20.5 ? O3' ADP 301 A 1 
HETATM 15 C C2' ADP . . . C 3 -2.136 20.805 22.845 1 22.97 ? C2' ADP 301 A 1 
HETATM 16 O O2' ADP . . . C 3 -2.348 20.525 21.473 1 22.44 ? O2' ADP 301 A 1 
HETATM 17 C C1' ADP . . . C 3 -0.628 20.698 23.032 1 21.28 ? C1' ADP 301 A 1 
HETATM 18 N N9 ADP . . . C 3 -0.18 20.007 24.261 1 19.74 ? N9 ADP 301 A 1 
HETATM 19 C C8 ADP . . . C 3 0.757 18.974 24.29 1 20.06 ? C8 ADP 301 A 1 
HETATM 20 N N7 ADP . . . C 3 0.981 18.568 25.541 1 20.46 ? N7 ADP 301 A 1 
HETATM 21 C C5 ADP . . . C 3 0.185 19.32 26.362 1 18.99 ? C5 ADP 301 A 1 
HETATM 22 C C6 ADP . . . C 3 0.035 19.318 27.763 1 20.68 ? C6 ADP 301 A 1 
HETATM 23 N N6 ADP . . . C 3 0.8 18.611 28.59 1 18.5 ? N6 ADP 301 A 1 
HETATM 24 N N1 ADP . . . C 3 -0.862 20.214 28.304 1 17.87 ? N1 ADP 301 A 1 
HETATM 25 C C2 ADP . . . C 3 -1.551 21.079 27.479 1 17.42 ? C2 ADP 301 A 1 
HETATM 26 N N3 ADP . . . C 3 -1.443 21.071 26.105 1 19.45 ? N3 ADP 301 A 1 
HETATM 27 C C4 ADP . . . C 3 -0.559 20.188 25.564 1 19.98 ? C4 ADP 301 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#