data_4DZY
#
_model_server_result.job_id            gUQuzu9RcydE1K77zfqkSw 
_model_server_result.datetime_utc      '2024-11-25 05:31:23' 
_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          4dzy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    4DZY 
#
_exptl.entry_id    4DZY 
_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            4DZY 
_cell.length_a            127.326 
_cell.length_b            127.326 
_cell.length_c            73.249 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DZY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        94 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 42 21 2' 
#
_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    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 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 OD1 ASN 279 A ASN 249 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc2 A O VAL 328 A VAL 298 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? 
metalc ? metalc3 A O ASP 330 A ASP 300 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? 
metalc ? metalc4 A O PHE 333 A PHE 303 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? 
metalc ? metalc5 A O GLY 367 A GLY 337 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.018 ? 
metalc ? metalc6 B O2B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc7 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
metalc ? metalc8 B O1A ADP . A ADP 401 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? 
metalc ? metalc9 C MG MG . A MG 402 1_555 F O HOH . A HOH 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc10 C MG MG . A MG 402 1_555 F O HOH . A HOH 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc11 C MG MG . A MG 402 1_555 F O HOH . A HOH 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
#
_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                     4DZY 
_atom_sites.fract_transf_matrix[1][1]    0.007854 
_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]    0.007854 
_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]    0.013652 
_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 1 ADP ADP . 
C 3 MG A 1 402 1 MG MG . 
D 4 K A 1 403 1 K K . 
E 5 WJ1 A 1 404 1 WJ1 WJ1 . 
F 6 HOH A 1 501 1 HOH HOH . 
F 6 HOH A 2 502 2 HOH HOH . 
F 6 HOH A 3 503 3 HOH HOH . 
F 6 HOH A 4 504 4 HOH HOH . 
F 6 HOH A 5 505 5 HOH HOH . 
F 6 HOH A 6 506 6 HOH HOH . 
F 6 HOH A 7 507 7 HOH HOH . 
F 6 HOH A 8 508 8 HOH HOH . 
F 6 HOH A 9 509 9 HOH HOH . 
F 6 HOH A 10 510 10 HOH HOH . 
F 6 HOH A 11 511 11 HOH HOH . 
F 6 HOH A 12 512 12 HOH HOH . 
F 6 HOH A 13 513 14 HOH HOH . 
F 6 HOH A 14 514 15 HOH HOH . 
F 6 HOH A 15 515 16 HOH HOH . 
F 6 HOH A 16 516 17 HOH HOH . 
F 6 HOH A 17 517 18 HOH HOH . 
F 6 HOH A 18 518 19 HOH HOH . 
F 6 HOH A 19 519 20 HOH HOH . 
F 6 HOH A 20 520 21 HOH HOH . 
F 6 HOH A 21 521 22 HOH HOH . 
F 6 HOH A 22 522 23 HOH HOH . 
F 6 HOH A 23 523 24 HOH HOH . 
F 6 HOH A 24 524 25 HOH HOH . 
F 6 HOH A 25 525 26 HOH HOH . 
F 6 HOH A 26 526 27 HOH HOH . 
F 6 HOH A 27 527 28 HOH HOH . 
F 6 HOH A 28 528 29 HOH HOH . 
F 6 HOH A 29 529 30 HOH HOH . 
F 6 HOH A 30 530 31 HOH HOH . 
F 6 HOH A 31 531 32 HOH HOH . 
F 6 HOH A 32 532 33 HOH HOH . 
F 6 HOH A 33 533 34 HOH HOH . 
F 6 HOH A 34 534 35 HOH HOH . 
F 6 HOH A 35 535 36 HOH HOH . 
F 6 HOH A 36 536 37 HOH HOH . 
F 6 HOH A 37 537 38 HOH HOH . 
F 6 HOH A 38 538 39 HOH HOH . 
F 6 HOH A 39 539 40 HOH HOH . 
F 6 HOH A 40 540 41 HOH HOH . 
F 6 HOH A 41 541 42 HOH HOH . 
F 6 HOH A 42 542 43 HOH HOH . 
F 6 HOH A 43 543 44 HOH HOH . 
F 6 HOH A 44 544 45 HOH HOH . 
F 6 HOH A 45 545 46 HOH HOH . 
F 6 HOH A 46 546 47 HOH HOH . 
F 6 HOH A 47 547 49 HOH HOH . 
F 6 HOH A 48 548 51 HOH HOH . 
F 6 HOH A 49 549 52 HOH HOH . 
F 6 HOH A 50 550 53 HOH HOH . 
F 6 HOH A 51 551 54 HOH HOH . 
F 6 HOH A 52 552 55 HOH HOH . 
F 6 HOH A 53 553 56 HOH HOH . 
F 6 HOH A 54 554 57 HOH HOH . 
F 6 HOH A 55 555 58 HOH HOH . 
F 6 HOH A 56 556 61 HOH HOH . 
F 6 HOH A 57 557 62 HOH HOH . 
F 6 HOH A 58 558 63 HOH HOH . 
F 6 HOH A 59 559 64 HOH HOH . 
F 6 HOH A 60 560 65 HOH HOH . 
F 6 HOH A 61 561 66 HOH HOH . 
F 6 HOH A 62 562 67 HOH HOH . 
F 6 HOH A 63 563 68 HOH HOH . 
F 6 HOH A 64 564 69 HOH HOH . 
F 6 HOH A 65 565 73 HOH HOH . 
F 6 HOH A 66 566 74 HOH HOH . 
F 6 HOH A 67 567 77 HOH HOH . 
F 6 HOH A 68 568 79 HOH HOH . 
F 6 HOH A 69 569 81 HOH HOH . 
F 6 HOH A 70 570 84 HOH HOH . 
F 6 HOH A 71 571 85 HOH HOH . 
F 6 HOH A 72 572 86 HOH HOH . 
F 6 HOH A 73 573 87 HOH HOH . 
F 6 HOH A 74 574 88 HOH HOH . 
F 6 HOH A 75 575 90 HOH HOH . 
F 6 HOH A 76 576 96 HOH HOH . 
F 6 HOH A 77 577 100 HOH HOH . 
F 6 HOH A 78 578 101 HOH HOH . 
F 6 HOH A 79 579 102 HOH HOH . 
F 6 HOH A 80 580 103 HOH HOH . 
F 6 HOH A 81 581 104 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 4.788 -32.767 -4.636 1 42.61 ? PB ADP 401 A 1 
HETATM 2 O O1B ADP . . . B 2 4.739 -32.383 -6.102 1 45.09 ? O1B ADP 401 A 1 
HETATM 3 O O2B ADP . . . B 2 6.131 -33.302 -4.231 1 42.11 ? O2B ADP 401 A 1 
HETATM 4 O O3B ADP . . . B 2 3.626 -33.605 -4.133 1 44.22 ? O3B ADP 401 A 1 
HETATM 5 P PA ADP . . . B 2 5.564 -30.4 -3.149 1 38.39 ? PA ADP 401 A 1 
HETATM 6 O O1A ADP . . . B 2 4.813 -29.224 -2.612 1 39.03 ? O1A ADP 401 A 1 
HETATM 7 O O2A ADP . . . B 2 6.392 -31.144 -2.142 1 42.94 ? O2A ADP 401 A 1 
HETATM 8 O O3A ADP . . . B 2 4.467 -31.364 -3.862 1 41.75 ? O3A ADP 401 A 1 
HETATM 9 O O5' ADP . . . B 2 6.535 -29.948 -4.37 1 40.3 ? O5' ADP 401 A 1 
HETATM 10 C C5' ADP . . . B 2 6.033 -29.185 -5.464 1 41.62 ? C5' ADP 401 A 1 
HETATM 11 C C4' ADP . . . B 2 6.963 -29.298 -6.66 1 45.46 ? C4' ADP 401 A 1 
HETATM 12 O O4' ADP . . . B 2 8.198 -28.649 -6.367 1 41.69 ? O4' ADP 401 A 1 
HETATM 13 C C3' ADP . . . B 2 7.352 -30.735 -6.979 1 41.6 ? C3' ADP 401 A 1 
HETATM 14 O O3' ADP . . . B 2 6.375 -31.382 -7.797 1 43.03 ? O3' ADP 401 A 1 
HETATM 15 C C2' ADP . . . B 2 8.669 -30.555 -7.698 1 46.32 ? C2' ADP 401 A 1 
HETATM 16 O O2' ADP . . . B 2 8.427 -30.205 -9.069 1 42.56 ? O2' ADP 401 A 1 
HETATM 17 C C1' ADP . . . B 2 9.255 -29.309 -7.059 1 40.46 ? C1' ADP 401 A 1 
HETATM 18 N N9 ADP . . . B 2 10.328 -29.567 -6.069 1 39.65 ? N9 ADP 401 A 1 
HETATM 19 C C8 ADP . . . B 2 10.195 -29.557 -4.728 1 40.41 ? C8 ADP 401 A 1 
HETATM 20 N N7 ADP . . . B 2 11.382 -29.809 -4.125 1 41.36 ? N7 ADP 401 A 1 
HETATM 21 C C5 ADP . . . B 2 12.287 -29.972 -5.105 1 39.46 ? C5 ADP 401 A 1 
HETATM 22 C C6 ADP . . . B 2 13.725 -30.25 -5.162 1 32.89 ? C6 ADP 401 A 1 
HETATM 23 N N6 ADP . . . B 2 14.425 -30.418 -4.02 1 32.86 ? N6 ADP 401 A 1 
HETATM 24 N N1 ADP . . . B 2 14.295 -30.351 -6.378 1 38.17 ? N1 ADP 401 A 1 
HETATM 25 C C2 ADP . . . B 2 13.585 -30.211 -7.511 1 39.13 ? C2 ADP 401 A 1 
HETATM 26 N N3 ADP . . . B 2 12.275 -29.956 -7.541 1 37.59 ? N3 ADP 401 A 1 
HETATM 27 C C4 ADP . . . B 2 11.594 -29.815 -6.38 1 41.58 ? C4 ADP 401 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#