data_5ORV
#
_model_server_result.job_id            IbdGCtoZihx0T_MQjytjZQ 
_model_server_result.datetime_utc      '2024-11-04 22:18:39' 
_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          5orv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    5ORV 
#
_exptl.entry_id    5ORV 
_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         120 
_cell.entry_id            5ORV 
_cell.length_a            81.66 
_cell.length_b            81.66 
_cell.length_c            175.15 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ORV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 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
covale ? covale1 A C THR 161 A THR 287 1_555 A N TPO 162 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 A C TPO 162 A TPO 288 1_555 A N LEU 163 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
metalc ? metalc1 A OD1 ASN 135 A ASN 261 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc2 A OD2 ASP 148 A ASP 274 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc3 A OD1 ASP 148 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? 
metalc ? metalc4 B O3B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc5 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc6 B O1B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc7 C MG MG . A MG 402 1_555 H O HOH . A HOH 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? 
metalc ? metalc8 C MG MG . A MG 402 1_555 H O HOH . A HOH 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc9 D MG MG . A MG 403 1_555 H O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc10 D MG MG . A MG 403 1_555 H O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc11 D MG MG . A MG 403 1_555 H O HOH . A HOH 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? 
metalc ? metalc12 D MG MG . A MG 403 1_555 H O HOH . A HOH 588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
#
_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 21 n n 
PB O2B ADP sing 22 n n 
PB O3B ADP sing 23 n n 
PB O3A ADP sing 24 n n 
O2B HOB2 ADP sing 25 n n 
O3B HOB3 ADP sing 26 n n 
PA O1A ADP doub 27 n n 
PA O2A ADP sing 28 n n 
PA O3A ADP sing 29 n n 
PA O5' ADP sing 30 n n 
O2A HOA2 ADP sing 31 n n 
O5' C5' ADP sing 32 n n 
C5' C4' ADP sing 33 n n 
C5' "H5'1" ADP sing 34 n n 
C5' "H5'2" ADP sing 35 n n 
C4' O4' ADP sing 36 n n 
C4' C3' ADP sing 37 n n 
C4' H4' ADP sing 38 n n 
O4' C1' ADP sing 39 n n 
C3' O3' ADP sing 40 n n 
C3' C2' ADP sing 41 n n 
C3' H3' ADP sing 42 n n 
O3' HO3' ADP sing 43 n n 
C2' O2' ADP sing 44 n n 
C2' C1' ADP sing 45 n n 
C2' H2' ADP sing 46 n n 
O2' HO2' ADP sing 47 n n 
C1' N9 ADP sing 48 n n 
C1' H1' ADP sing 49 n n 
N9 C8 ADP sing 50 n y 
N9 C4 ADP sing 51 n y 
C8 N7 ADP doub 52 n y 
C8 H8 ADP sing 53 n n 
N7 C5 ADP sing 54 n y 
C5 C6 ADP sing 55 n y 
C5 C4 ADP doub 56 n y 
C6 N6 ADP sing 57 n n 
C6 N1 ADP doub 58 n y 
N6 HN61 ADP sing 59 n n 
N6 HN62 ADP sing 60 n n 
N1 C2 ADP sing 61 n y 
C2 N3 ADP doub 62 n y 
C2 H2 ADP sing 63 n n 
N3 C4 ADP sing 64 n y 
#
_atom_sites.entry_id                     5ORV 
_atom_sites.fract_transf_matrix[1][1]    0.012246 
_atom_sites.fract_transf_matrix[1][2]    0.00707 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01414 
_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]    0.005709 
_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 1392 ADP ADP . 
C 3 MG A 1 402 1395 MG MG . 
D 3 MG A 1 403 1396 MG MG . 
E 4 CL A 1 404 1397 CL CL . 
F 4 CL A 1 405 1398 CL CL . 
G 5 A65 A 1 406 1 A65 FRG . 
H 6 HOH A 1 501 6 HOH HOH . 
H 6 HOH A 2 502 57 HOH HOH . 
H 6 HOH A 3 503 63 HOH HOH . 
H 6 HOH A 4 504 93 HOH HOH . 
H 6 HOH A 5 505 80 HOH HOH . 
H 6 HOH A 6 506 71 HOH HOH . 
H 6 HOH A 7 507 62 HOH HOH . 
H 6 HOH A 8 508 7 HOH HOH . 
H 6 HOH A 9 509 76 HOH HOH . 
H 6 HOH A 10 510 30 HOH HOH . 
H 6 HOH A 11 511 2 HOH HOH . 
H 6 HOH A 12 512 12 HOH HOH . 
H 6 HOH A 13 513 103 HOH HOH . 
H 6 HOH A 14 514 36 HOH HOH . 
H 6 HOH A 15 515 64 HOH HOH . 
H 6 HOH A 16 516 55 HOH HOH . 
H 6 HOH A 17 517 52 HOH HOH . 
H 6 HOH A 18 518 39 HOH HOH . 
H 6 HOH A 19 519 9 HOH HOH . 
H 6 HOH A 20 520 14 HOH HOH . 
H 6 HOH A 21 521 17 HOH HOH . 
H 6 HOH A 22 522 29 HOH HOH . 
H 6 HOH A 23 523 18 HOH HOH . 
H 6 HOH A 24 524 40 HOH HOH . 
H 6 HOH A 25 525 56 HOH HOH . 
H 6 HOH A 26 526 5 HOH HOH . 
H 6 HOH A 27 527 77 HOH HOH . 
H 6 HOH A 28 528 37 HOH HOH . 
H 6 HOH A 29 529 22 HOH HOH . 
H 6 HOH A 30 530 15 HOH HOH . 
H 6 HOH A 31 531 16 HOH HOH . 
H 6 HOH A 32 532 50 HOH HOH . 
H 6 HOH A 33 533 43 HOH HOH . 
H 6 HOH A 34 534 27 HOH HOH . 
H 6 HOH A 35 535 1 HOH HOH . 
H 6 HOH A 36 536 42 HOH HOH . 
H 6 HOH A 37 537 21 HOH HOH . 
H 6 HOH A 38 538 106 HOH HOH . 
H 6 HOH A 39 539 23 HOH HOH . 
H 6 HOH A 40 540 82 HOH HOH . 
H 6 HOH A 41 541 73 HOH HOH . 
H 6 HOH A 42 542 85 HOH HOH . 
H 6 HOH A 43 543 78 HOH HOH . 
H 6 HOH A 44 544 26 HOH HOH . 
H 6 HOH A 45 545 38 HOH HOH . 
H 6 HOH A 46 546 104 HOH HOH . 
H 6 HOH A 47 547 41 HOH HOH . 
H 6 HOH A 48 548 68 HOH HOH . 
H 6 HOH A 49 549 25 HOH HOH . 
H 6 HOH A 50 550 20 HOH HOH . 
H 6 HOH A 51 551 46 HOH HOH . 
H 6 HOH A 52 552 3 HOH HOH . 
H 6 HOH A 53 553 89 HOH HOH . 
H 6 HOH A 54 554 45 HOH HOH . 
H 6 HOH A 55 555 28 HOH HOH . 
H 6 HOH A 56 556 58 HOH HOH . 
H 6 HOH A 57 557 13 HOH HOH . 
H 6 HOH A 58 558 11 HOH HOH . 
H 6 HOH A 59 559 33 HOH HOH . 
H 6 HOH A 60 560 4 HOH HOH . 
H 6 HOH A 61 561 35 HOH HOH . 
H 6 HOH A 62 562 32 HOH HOH . 
H 6 HOH A 63 563 10 HOH HOH . 
H 6 HOH A 64 564 69 HOH HOH . 
H 6 HOH A 65 565 90 HOH HOH . 
H 6 HOH A 66 566 86 HOH HOH . 
H 6 HOH A 67 567 79 HOH HOH . 
H 6 HOH A 68 568 31 HOH HOH . 
H 6 HOH A 69 569 34 HOH HOH . 
H 6 HOH A 70 570 44 HOH HOH . 
H 6 HOH A 71 571 75 HOH HOH . 
H 6 HOH A 72 572 24 HOH HOH . 
H 6 HOH A 73 573 72 HOH HOH . 
H 6 HOH A 74 574 48 HOH HOH . 
H 6 HOH A 75 575 8 HOH HOH . 
H 6 HOH A 76 576 100 HOH HOH . 
H 6 HOH A 77 577 19 HOH HOH . 
H 6 HOH A 78 578 95 HOH HOH . 
H 6 HOH A 79 579 51 HOH HOH . 
H 6 HOH A 80 580 53 HOH HOH . 
H 6 HOH A 81 581 111 HOH HOH . 
H 6 HOH A 82 582 74 HOH HOH . 
H 6 HOH A 83 583 70 HOH HOH . 
H 6 HOH A 84 584 112 HOH HOH . 
H 6 HOH A 85 585 98 HOH HOH . 
H 6 HOH A 86 586 61 HOH HOH . 
H 6 HOH A 87 587 97 HOH HOH . 
H 6 HOH A 88 588 96 HOH HOH . 
H 6 HOH A 89 589 83 HOH HOH . 
H 6 HOH A 90 590 99 HOH HOH . 
H 6 HOH A 91 591 59 HOH HOH . 
H 6 HOH A 92 592 114 HOH HOH . 
H 6 HOH A 93 593 113 HOH HOH . 
H 6 HOH A 94 594 49 HOH HOH . 
H 6 HOH A 95 595 47 HOH HOH . 
H 6 HOH A 96 596 81 HOH HOH . 
H 6 HOH A 97 597 115 HOH HOH . 
H 6 HOH A 98 598 94 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 -12.257 23.952 -6.08 1 44.5 ? PB ADP 401 A 1 
HETATM 2 O O1B ADP . . . B 2 -12.941 23.51 -7.345 1 40.13 ? O1B ADP 401 A 1 
HETATM 3 O O2B ADP . . . B 2 -11.719 22.757 -5.33 1 44.43 ? O2B ADP 401 A 1 
HETATM 4 O O3B ADP . . . B 2 -13.028 24.928 -5.215 1 38.15 ? O3B ADP 401 A 1 
HETATM 5 P PA ADP . . . B 2 -10.858 26.275 -7.13 1 35.47 ? PA ADP 401 A 1 
HETATM 6 O O1A ADP . . . B 2 -10.668 26.332 -8.635 1 39.95 ? O1A ADP 401 A 1 
HETATM 7 O O2A ADP . . . B 2 -11.877 27.218 -6.54 1 36.79 ? O2A ADP 401 A 1 
HETATM 8 O O3A ADP . . . B 2 -10.933 24.772 -6.554 1 36.27 ? O3A ADP 401 A 1 
HETATM 9 O O5' ADP . . . B 2 -9.452 26.799 -6.513 1 35.89 ? O5' ADP 401 A 1 
HETATM 10 C C5' ADP . . . B 2 -9.302 26.722 -5.086 1 36.28 ? C5' ADP 401 A 1 
HETATM 11 C C4' ADP . . . B 2 -8.497 27.883 -4.496 1 36.64 ? C4' ADP 401 A 1 
HETATM 12 O O4' ADP . . . B 2 -7.175 28.021 -5.051 1 35.83 ? O4' ADP 401 A 1 
HETATM 13 C C3' ADP . . . B 2 -9.183 29.213 -4.73 1 36.18 ? C3' ADP 401 A 1 
HETATM 14 O O3' ADP . . . B 2 -10.195 29.429 -3.734 1 37.83 ? O3' ADP 401 A 1 
HETATM 15 C C2' ADP . . . B 2 -8.002 30.171 -4.651 1 37.39 ? C2' ADP 401 A 1 
HETATM 16 O O2' ADP . . . B 2 -7.649 30.383 -3.277 1 36.4 ? O2' ADP 401 A 1 
HETATM 17 C C1' ADP . . . B 2 -6.864 29.397 -5.287 1 33.88 ? C1' ADP 401 A 1 
HETATM 18 N N9 ADP . . . B 2 -6.834 29.581 -6.763 1 33.99 ? N9 ADP 401 A 1 
HETATM 19 C C8 ADP . . . B 2 -7.532 28.837 -7.647 1 33.51 ? C8 ADP 401 A 1 
HETATM 20 N N7 ADP . . . B 2 -7.293 29.23 -8.92 1 33.66 ? N7 ADP 401 A 1 
HETATM 21 C C5 ADP . . . B 2 -6.407 30.247 -8.854 1 32.72 ? C5 ADP 401 A 1 
HETATM 22 C C6 ADP . . . B 2 -5.715 31.094 -9.846 1 35.26 ? C6 ADP 401 A 1 
HETATM 23 N N6 ADP . . . B 2 -5.971 30.924 -11.17 1 36.77 ? N6 ADP 401 A 1 
HETATM 24 N N1 ADP . . . B 2 -4.856 32.047 -9.393 1 34.34 ? N1 ADP 401 A 1 
HETATM 25 C C2 ADP . . . B 2 -4.631 32.207 -8.064 1 34.26 ? C2 ADP 401 A 1 
HETATM 26 N N3 ADP . . . B 2 -5.21 31.449 -7.102 1 35.35 ? N3 ADP 401 A 1 
HETATM 27 C C4 ADP . . . B 2 -6.098 30.467 -7.434 1 35.09 ? C4 ADP 401 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           36 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           27 
#