data_5ZO9
#
_model_server_result.job_id            CB7pe-w2uSNA1JzaUrObdQ 
_model_server_result.datetime_utc      '2024-10-22 03:41:35' 
_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          5zo9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":600}' 
#
_entry.id    5ZO9 
#
_exptl.entry_id    5ZO9 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          102.19 
_cell.angle_gamma         90 
_cell.entry_id            5ZO9 
_cell.length_a            155.158 
_cell.length_b            50.729 
_cell.length_c            94.309 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ZO9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,O 1 1 
B,I,J,K,L,M,N,P 2 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
? 2 C N N 
? 2 I 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 A OG1 THR 103 A THR 112 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc2 A OE1 GLU 158 A GLU 167 1_555 H NA NA . A NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? 
metalc ? metalc3 C O1B ADP . A ADP 600 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc4 D MG MG . A MG 601 1_555 O O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? 
metalc ? metalc5 G O1 SO4 . A SO4 604 1_555 H NA NA . A NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.02 ? 
metalc ? metalc6 B OG1 THR 103 B THR 112 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc7 B OE1 GLU 158 B GLU 167 1_555 N NA NA . B NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? 
metalc ? metalc8 I O2B ADP . B ADP 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? 
metalc ? metalc9 J MG MG . B MG 601 1_555 P O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? 
metalc ? metalc10 M O4 SO4 . B SO4 604 1_555 N NA NA . B NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? 
#
_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 54 n n 
PB O2B ADP sing 55 n n 
PB O3B ADP sing 56 n n 
PB O3A ADP sing 57 n n 
O2B HOB2 ADP sing 58 n n 
O3B HOB3 ADP sing 59 n n 
PA O1A ADP doub 60 n n 
PA O2A ADP sing 61 n n 
PA O3A ADP sing 62 n n 
PA O5' ADP sing 63 n n 
O2A HOA2 ADP sing 64 n n 
O5' C5' ADP sing 65 n n 
C5' C4' ADP sing 66 n n 
C5' "H5'1" ADP sing 67 n n 
C5' "H5'2" ADP sing 68 n n 
C4' O4' ADP sing 69 n n 
C4' C3' ADP sing 70 n n 
C4' H4' ADP sing 71 n n 
O4' C1' ADP sing 72 n n 
C3' O3' ADP sing 73 n n 
C3' C2' ADP sing 74 n n 
C3' H3' ADP sing 75 n n 
O3' HO3' ADP sing 76 n n 
C2' O2' ADP sing 77 n n 
C2' C1' ADP sing 78 n n 
C2' H2' ADP sing 79 n n 
O2' HO2' ADP sing 80 n n 
C1' N9 ADP sing 81 n n 
C1' H1' ADP sing 82 n n 
N9 C8 ADP sing 83 n y 
N9 C4 ADP sing 84 n y 
C8 N7 ADP doub 85 n y 
C8 H8 ADP sing 86 n n 
N7 C5 ADP sing 87 n y 
C5 C6 ADP sing 88 n y 
C5 C4 ADP doub 89 n y 
C6 N6 ADP sing 90 n n 
C6 N1 ADP doub 91 n y 
N6 HN61 ADP sing 92 n n 
N6 HN62 ADP sing 93 n n 
N1 C2 ADP sing 94 n y 
C2 N3 ADP doub 95 n y 
C2 H2 ADP sing 96 n n 
N3 C4 ADP sing 97 n y 
#
_atom_sites.entry_id                     5ZO9 
_atom_sites.fract_transf_matrix[1][1]    0.006445 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001392 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019713 
_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]    0.010848 
_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 2 ADP A 1 600 600 ADP ADP . 
D 3 MG A 1 601 601 MG MG . 
E 4 4C5 A 1 602 602 4C5 4C5 . 
F 5 SO4 A 1 603 603 SO4 SO4 . 
G 5 SO4 A 1 604 604 SO4 SO4 . 
H 6 NA A 1 605 605 NA NA . 
I 2 ADP B 1 600 600 ADP ADP . 
J 3 MG B 1 601 601 MG MG . 
K 4 4C5 B 1 602 602 4C5 4C5 . 
L 5 SO4 B 1 603 603 SO4 SO4 . 
M 5 SO4 B 1 604 604 SO4 SO4 . 
N 6 NA B 1 605 605 NA NA . 
O 7 HOH A 1 701 18 HOH HOH . 
O 7 HOH A 2 702 6 HOH HOH . 
O 7 HOH A 3 703 5 HOH HOH . 
O 7 HOH A 4 704 17 HOH HOH . 
O 7 HOH A 5 705 7 HOH HOH . 
O 7 HOH A 6 706 10 HOH HOH . 
O 7 HOH A 7 707 13 HOH HOH . 
O 7 HOH A 8 708 9 HOH HOH . 
O 7 HOH A 9 709 1 HOH HOH . 
P 7 HOH B 1 701 15 HOH HOH . 
P 7 HOH B 2 702 4 HOH HOH . 
P 7 HOH B 3 703 14 HOH HOH . 
P 7 HOH B 4 704 16 HOH HOH . 
P 7 HOH B 5 705 8 HOH HOH . 
P 7 HOH B 6 706 12 HOH HOH . 
P 7 HOH B 7 707 11 HOH HOH . 
P 7 HOH B 8 708 3 HOH HOH . 
P 7 HOH B 9 709 2 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 . . . I 2 39.264 -12.514 46.106 1 41.63 ? PB ADP 600 B 1 
HETATM 2 O O1B ADP . . . I 2 39.999 -12.504 44.804 1 39.41 ? O1B ADP 600 B 1 
HETATM 3 O O2B ADP . . . I 2 39.643 -11.508 47.184 1 32.24 ? O2B ADP 600 B 1 
HETATM 4 O O3B ADP . . . I 2 37.749 -12.58 45.835 1 37.85 ? O3B ADP 600 B 1 
HETATM 5 P PA ADP . . . I 2 40.059 -14.353 48.062 1 40.72 ? PA ADP 600 B 1 
HETATM 6 O O1A ADP . . . I 2 41.352 -13.689 48.527 1 38.69 ? O1A ADP 600 B 1 
HETATM 7 O O2A ADP . . . I 2 38.761 -14.011 48.794 1 29.17 ? O2A ADP 600 B 1 
HETATM 8 O O3A ADP . . . I 2 39.828 -13.978 46.515 1 38.01 ? O3A ADP 600 B 1 
HETATM 9 O O5' ADP . . . I 2 40.403 -15.939 47.955 1 36.37 ? O5' ADP 600 B 1 
HETATM 10 C C5' ADP . . . I 2 39.362 -16.888 47.731 1 41.04 ? C5' ADP 600 B 1 
HETATM 11 C C4' ADP . . . I 2 39.634 -18.253 48.365 1 42.38 ? C4' ADP 600 B 1 
HETATM 12 O O4' ADP . . . I 2 40.58 -19.024 47.577 1 41.79 ? O4' ADP 600 B 1 
HETATM 13 C C3' ADP . . . I 2 40.229 -18.138 49.759 1 41 ? C3' ADP 600 B 1 
HETATM 14 O O3' ADP . . . I 2 39.812 -19.259 50.503 1 38.13 ? O3' ADP 600 B 1 
HETATM 15 C C2' ADP . . . I 2 41.714 -18.281 49.553 1 42.49 ? C2' ADP 600 B 1 
HETATM 16 O O2' ADP . . . I 2 42.388 -18.797 50.704 1 41.6 ? O2' ADP 600 B 1 
HETATM 17 C C1' ADP . . . I 2 41.778 -19.223 48.345 1 44.44 ? C1' ADP 600 B 1 
HETATM 18 N N9 ADP . . . I 2 42.966 -18.884 47.537 1 47.45 ? N9 ADP 600 B 1 
HETATM 19 C C8 ADP . . . I 2 43.059 -17.86 46.648 1 50.22 ? C8 ADP 600 B 1 
HETATM 20 N N7 ADP . . . I 2 44.284 -17.827 46.061 1 46.6 ? N7 ADP 600 B 1 
HETATM 21 C C5 ADP . . . I 2 44.972 -18.84 46.591 1 46.66 ? C5 ADP 600 B 1 
HETATM 22 C C6 ADP . . . I 2 46.326 -19.368 46.416 1 47.96 ? C6 ADP 600 B 1 
HETATM 23 N N6 ADP . . . I 2 47.131 -18.73 45.541 1 44.36 ? N6 ADP 600 B 1 
HETATM 24 N N1 ADP . . . I 2 46.683 -20.471 47.159 1 49.3 ? N1 ADP 600 B 1 
HETATM 25 C C2 ADP . . . I 2 45.836 -21.068 48.028 1 43.31 ? C2 ADP 600 B 1 
HETATM 26 N N3 ADP . . . I 2 44.583 -20.626 48.227 1 43.27 ? N3 ADP 600 B 1 
HETATM 27 C C4 ADP . . . I 2 44.113 -19.543 47.561 1 45.13 ? C4 ADP 600 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#