data_3DKP
#
_model_server_result.job_id            tppLJVYXk-ovehHx_FGqWw 
_model_server_result.datetime_utc      '2025-03-04 11:56:19' 
_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          3dkp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    3DKP 
#
_exptl.entry_id    3DKP 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.37 
_cell.angle_gamma         90 
_cell.entry_id            3DKP 
_cell.length_a            40.63 
_cell.length_b            38.36 
_cell.length_c            73.84 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DKP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D N 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 B MG MG . A MG 401 1_555 C O1B ADP . A ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc2 B MG MG . A MG 401 1_555 F O HOH . A HOH 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc3 B MG MG . A MG 401 1_555 F O HOH . A HOH 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc4 B MG MG . A MG 401 1_555 F O HOH . A HOH 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? 
metalc ? metalc5 B MG MG . A MG 401 1_555 F O HOH . A HOH 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc6 B MG MG . A MG 401 1_555 F O HOH . A HOH 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? 
#
_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                     3DKP 
_atom_sites.fract_transf_matrix[1][1]    0.024612 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00016 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.026069 
_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]    0.013543 
_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 ADP A 1 402 1 ADP ADP . 
D 3 ADP A 1 403 2 ADP ADP . 
E 4 GOL A 1 404 1 GOL GOL . 
F 5 HOH A 1 405 1 HOH HOH . 
F 5 HOH A 2 406 2 HOH HOH . 
F 5 HOH A 3 407 3 HOH HOH . 
F 5 HOH A 4 408 4 HOH HOH . 
F 5 HOH A 5 409 5 HOH HOH . 
F 5 HOH A 6 410 6 HOH HOH . 
F 5 HOH A 7 411 7 HOH HOH . 
F 5 HOH A 8 412 8 HOH HOH . 
F 5 HOH A 9 413 9 HOH HOH . 
F 5 HOH A 10 414 10 HOH HOH . 
F 5 HOH A 11 415 11 HOH HOH . 
F 5 HOH A 12 416 12 HOH HOH . 
F 5 HOH A 13 417 13 HOH HOH . 
F 5 HOH A 14 418 14 HOH HOH . 
F 5 HOH A 15 419 15 HOH HOH . 
F 5 HOH A 16 420 16 HOH HOH . 
F 5 HOH A 17 421 17 HOH HOH . 
F 5 HOH A 18 422 18 HOH HOH . 
F 5 HOH A 19 423 19 HOH HOH . 
F 5 HOH A 20 424 20 HOH HOH . 
F 5 HOH A 21 425 21 HOH HOH . 
F 5 HOH A 22 426 22 HOH HOH . 
F 5 HOH A 23 427 23 HOH HOH . 
F 5 HOH A 24 428 24 HOH HOH . 
F 5 HOH A 25 429 25 HOH HOH . 
F 5 HOH A 26 430 26 HOH HOH . 
F 5 HOH A 27 431 27 HOH HOH . 
F 5 HOH A 28 432 28 HOH HOH . 
F 5 HOH A 29 433 29 HOH HOH . 
F 5 HOH A 30 434 30 HOH HOH . 
F 5 HOH A 31 435 31 HOH HOH . 
F 5 HOH A 32 436 32 HOH HOH . 
F 5 HOH A 33 437 33 HOH HOH . 
F 5 HOH A 34 438 34 HOH HOH . 
F 5 HOH A 35 439 35 HOH HOH . 
F 5 HOH A 36 440 36 HOH HOH . 
F 5 HOH A 37 441 37 HOH HOH . 
F 5 HOH A 38 442 38 HOH HOH . 
F 5 HOH A 39 443 39 HOH HOH . 
F 5 HOH A 40 444 40 HOH HOH . 
F 5 HOH A 41 445 41 HOH HOH . 
F 5 HOH A 42 446 42 HOH HOH . 
F 5 HOH A 43 447 43 HOH HOH . 
F 5 HOH A 44 448 44 HOH HOH . 
F 5 HOH A 45 449 45 HOH HOH . 
F 5 HOH A 46 450 46 HOH HOH . 
F 5 HOH A 47 451 47 HOH HOH . 
F 5 HOH A 48 452 48 HOH HOH . 
F 5 HOH A 49 453 49 HOH HOH . 
F 5 HOH A 50 454 50 HOH HOH . 
F 5 HOH A 51 455 51 HOH HOH . 
F 5 HOH A 52 456 52 HOH HOH . 
F 5 HOH A 53 457 53 HOH HOH . 
F 5 HOH A 54 458 54 HOH HOH . 
F 5 HOH A 55 459 55 HOH HOH . 
F 5 HOH A 56 460 56 HOH HOH . 
F 5 HOH A 57 461 57 HOH HOH . 
F 5 HOH A 58 462 58 HOH HOH . 
F 5 HOH A 59 463 59 HOH HOH . 
F 5 HOH A 60 464 60 HOH HOH . 
F 5 HOH A 61 465 61 HOH HOH . 
F 5 HOH A 62 466 62 HOH HOH . 
F 5 HOH A 63 467 63 HOH HOH . 
F 5 HOH A 64 468 64 HOH HOH . 
F 5 HOH A 65 469 65 HOH HOH . 
F 5 HOH A 66 470 66 HOH HOH . 
F 5 HOH A 67 471 67 HOH HOH . 
F 5 HOH A 68 472 68 HOH HOH . 
F 5 HOH A 69 473 69 HOH HOH . 
F 5 HOH A 70 474 70 HOH HOH . 
F 5 HOH A 71 475 71 HOH HOH . 
F 5 HOH A 72 476 72 HOH HOH . 
F 5 HOH A 73 477 73 HOH HOH . 
F 5 HOH A 74 478 74 HOH HOH . 
F 5 HOH A 75 479 75 HOH HOH . 
F 5 HOH A 76 480 76 HOH HOH . 
F 5 HOH A 77 481 77 HOH HOH . 
F 5 HOH A 78 482 78 HOH HOH . 
F 5 HOH A 79 483 79 HOH HOH . 
F 5 HOH A 80 484 80 HOH HOH . 
F 5 HOH A 81 485 81 HOH HOH . 
F 5 HOH A 82 486 82 HOH HOH . 
F 5 HOH A 83 487 83 HOH HOH . 
F 5 HOH A 84 488 84 HOH HOH . 
F 5 HOH A 85 489 85 HOH HOH . 
F 5 HOH A 86 490 86 HOH HOH . 
F 5 HOH A 87 491 87 HOH HOH . 
F 5 HOH A 88 492 88 HOH HOH . 
F 5 HOH A 89 493 89 HOH HOH . 
F 5 HOH A 90 494 90 HOH HOH . 
F 5 HOH A 91 495 91 HOH HOH . 
F 5 HOH A 92 496 92 HOH HOH . 
F 5 HOH A 93 497 93 HOH HOH . 
F 5 HOH A 94 498 94 HOH HOH . 
F 5 HOH A 95 499 95 HOH HOH . 
F 5 HOH A 96 500 96 HOH HOH . 
F 5 HOH A 97 501 97 HOH HOH . 
F 5 HOH A 98 502 98 HOH HOH . 
F 5 HOH A 99 503 99 HOH HOH . 
F 5 HOH A 100 504 100 HOH HOH . 
F 5 HOH A 101 505 101 HOH HOH . 
F 5 HOH A 102 506 102 HOH HOH . 
F 5 HOH A 103 507 103 HOH HOH . 
F 5 HOH A 104 508 104 HOH HOH . 
F 5 HOH A 105 509 105 HOH HOH . 
F 5 HOH A 106 510 106 HOH HOH . 
F 5 HOH A 107 511 107 HOH HOH . 
F 5 HOH A 108 512 108 HOH HOH . 
F 5 HOH A 109 513 109 HOH HOH . 
F 5 HOH A 110 514 110 HOH HOH . 
F 5 HOH A 111 515 111 HOH HOH . 
F 5 HOH A 112 516 112 HOH HOH . 
F 5 HOH A 113 517 113 HOH HOH . 
F 5 HOH A 114 518 114 HOH HOH . 
F 5 HOH A 115 519 115 HOH HOH . 
F 5 HOH A 116 520 116 HOH HOH . 
F 5 HOH A 117 521 117 HOH HOH . 
F 5 HOH A 118 522 118 HOH HOH . 
F 5 HOH A 119 523 119 HOH HOH . 
F 5 HOH A 120 524 120 HOH HOH . 
F 5 HOH A 121 525 121 HOH HOH . 
F 5 HOH A 122 526 122 HOH HOH . 
F 5 HOH A 123 527 123 HOH HOH . 
F 5 HOH A 124 528 124 HOH HOH . 
F 5 HOH A 125 529 125 HOH HOH . 
F 5 HOH A 126 530 126 HOH HOH . 
F 5 HOH A 127 531 127 HOH HOH . 
F 5 HOH A 128 532 128 HOH HOH . 
F 5 HOH A 129 533 129 HOH HOH . 
F 5 HOH A 130 534 130 HOH HOH . 
F 5 HOH A 131 535 131 HOH HOH . 
F 5 HOH A 132 536 132 HOH HOH . 
F 5 HOH A 133 537 133 HOH HOH . 
F 5 HOH A 134 538 134 HOH HOH . 
F 5 HOH A 135 539 135 HOH HOH . 
F 5 HOH A 136 540 136 HOH HOH . 
F 5 HOH A 137 541 137 HOH HOH . 
F 5 HOH A 138 542 138 HOH HOH . 
F 5 HOH A 139 543 139 HOH HOH . 
F 5 HOH A 140 544 140 HOH HOH . 
F 5 HOH A 141 545 141 HOH HOH . 
F 5 HOH A 142 546 142 HOH HOH . 
F 5 HOH A 143 547 143 HOH HOH . 
F 5 HOH A 144 548 144 HOH HOH . 
F 5 HOH A 145 549 145 HOH HOH . 
F 5 HOH A 146 550 146 HOH HOH . 
F 5 HOH A 147 551 147 HOH HOH . 
F 5 HOH A 148 552 148 HOH HOH . 
F 5 HOH A 149 553 149 HOH HOH . 
F 5 HOH A 150 554 150 HOH HOH . 
F 5 HOH A 151 555 151 HOH HOH . 
F 5 HOH A 152 556 152 HOH HOH . 
F 5 HOH A 153 557 153 HOH HOH . 
F 5 HOH A 154 558 154 HOH HOH . 
F 5 HOH A 155 559 155 HOH HOH . 
F 5 HOH A 156 560 156 HOH HOH . 
F 5 HOH A 157 561 157 HOH HOH . 
F 5 HOH A 158 562 158 HOH HOH . 
F 5 HOH A 159 563 159 HOH HOH . 
F 5 HOH A 160 564 160 HOH HOH . 
F 5 HOH A 161 565 161 HOH HOH . 
F 5 HOH A 162 566 162 HOH HOH . 
F 5 HOH A 163 567 163 HOH HOH . 
F 5 HOH A 164 568 164 HOH HOH . 
F 5 HOH A 165 569 165 HOH HOH . 
F 5 HOH A 166 570 166 HOH HOH . 
F 5 HOH A 167 571 167 HOH HOH . 
F 5 HOH A 168 572 168 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 10.681 -7.879 19.166 1 2 ? PB ADP 402 A 1 
HETATM 2 O O1B ADP . . . C 3 11.153 -6.558 19.637 1 3.32 ? O1B ADP 402 A 1 
HETATM 3 O O2B ADP . . . C 3 9.227 -7.807 18.541 1 2 ? O2B ADP 402 A 1 
HETATM 4 O O3B ADP . . . C 3 10.702 -9.058 20.281 1 5.86 ? O3B ADP 402 A 1 
HETATM 5 P PA ADP . . . C 3 13.053 -8.061 17.597 1 2 ? PA ADP 402 A 1 
HETATM 6 O O1A ADP . . . C 3 13.18 -6.644 17.138 1 4.96 ? O1A ADP 402 A 1 
HETATM 7 O O2A ADP . . . C 3 13.953 -8.317 18.881 1 2 ? O2A ADP 402 A 1 
HETATM 8 O O3A ADP . . . C 3 11.541 -8.523 17.947 1 3.6 ? O3A ADP 402 A 1 
HETATM 9 O O5' ADP . . . C 3 13.45 -9.065 16.445 1 2.62 ? O5' ADP 402 A 1 
HETATM 10 C C5' ADP . . . C 3 13.572 -10.465 16.791 1 6.29 ? C5' ADP 402 A 1 
HETATM 11 C C4' ADP . . . C 3 14.405 -11.241 15.752 1 6.44 ? C4' ADP 402 A 1 
HETATM 12 O O4' ADP . . . C 3 13.761 -11.091 14.469 1 7.05 ? O4' ADP 402 A 1 
HETATM 13 C C3' ADP . . . C 3 15.765 -10.537 15.667 1 7.79 ? C3' ADP 402 A 1 
HETATM 14 O O3' ADP . . . C 3 16.8 -11.538 15.646 1 10.66 ? O3' ADP 402 A 1 
HETATM 15 C C2' ADP . . . C 3 15.701 -9.792 14.342 1 7.52 ? C2' ADP 402 A 1 
HETATM 16 O O2' ADP . . . C 3 16.967 -9.859 13.726 1 9.28 ? O2' ADP 402 A 1 
HETATM 17 C C1' ADP . . . C 3 14.776 -10.648 13.531 1 5.59 ? C1' ADP 402 A 1 
HETATM 18 N N9 ADP . . . C 3 14.093 -9.862 12.455 1 4.67 ? N9 ADP 402 A 1 
HETATM 19 C C8 ADP . . . C 3 13.61 -8.609 12.502 1 2.34 ? C8 ADP 402 A 1 
HETATM 20 N N7 ADP . . . C 3 13.068 -8.309 11.324 1 2.54 ? N7 ADP 402 A 1 
HETATM 21 C C5 ADP . . . C 3 13.197 -9.4 10.543 1 3.41 ? C5 ADP 402 A 1 
HETATM 22 C C6 ADP . . . C 3 12.839 -9.704 9.239 1 2.6 ? C6 ADP 402 A 1 
HETATM 23 N N6 ADP . . . C 3 12.184 -8.812 8.454 1 2 ? N6 ADP 402 A 1 
HETATM 24 N N1 ADP . . . C 3 13.139 -10.928 8.778 1 2.87 ? N1 ADP 402 A 1 
HETATM 25 C C2 ADP . . . C 3 13.762 -11.844 9.51 1 3.83 ? C2 ADP 402 A 1 
HETATM 26 N N3 ADP . . . C 3 14.126 -11.574 10.748 1 3.68 ? N3 ADP 402 A 1 
HETATM 27 C C4 ADP . . . C 3 13.846 -10.372 11.271 1 2.48 ? C4 ADP 402 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           27 
#