data_5J7I
#
_model_server_result.job_id            '_vlEf_VQo1D46aVWqQkTIw' 
_model_server_result.datetime_utc      '2024-11-23 22:05:07' 
_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          5j7i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":501}' 
#
_entry.id    5J7I 
#
_exptl.entry_id    5J7I 
_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    3 
_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            5J7I 
_cell.length_a            93.054 
_cell.length_b            109.543 
_cell.length_c            204.149 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5J7I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 G N N 
? 2 H 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
covale ? covale1 A C ILE 272 A ILE 272 1_555 A N SCY 273 A SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 A C SCY 273 A SCY 273 1_555 A N ALA 274 A ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale3 B C ILE 272 B ILE 272 1_555 B N SCY 273 B SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 B C SCY 273 B SCY 273 1_555 B N ALA 274 B ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale5 C C ILE 272 C ILE 272 1_555 C N SCY 273 C SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale6 C C SCY 273 C SCY 273 1_555 C N ALA 274 C ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale7 D C ILE 272 D ILE 272 1_555 D N SCY 273 D SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale8 D C SCY 273 D SCY 273 1_555 D N ALA 274 D ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
#
_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                     5J7I 
_atom_sites.fract_transf_matrix[1][1]    0.010746 
_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]    0.009129 
_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]    0.004898 
_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
E 2 ADP A 1 501 1 ADP ADP . 
F 3 APR B 1 501 2 APR APR . 
G 2 ADP C 1 501 3 ADP ADP . 
H 2 ADP D 1 501 4 ADP ADP . 
#
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 . . . H 2 37.366 -2.297 -48.72 1 55.32 ? PB ADP 501 D 1 
HETATM 2 O O1B ADP . . . H 2 37.865 -2.481 -50.138 1 55.32 ? O1B ADP 501 D 1 
HETATM 3 O O2B ADP . . . H 2 38.372 -1.622 -47.804 1 55.32 ? O2B ADP 501 D 1 
HETATM 4 O O3B ADP . . . H 2 35.978 -1.696 -48.631 1 55.32 ? O3B ADP 501 D 1 
HETATM 5 P PA ADP . . . H 2 35.878 -4.454 -47.516 1 55.32 ? PA ADP 501 D 1 
HETATM 6 O O1A ADP . . . H 2 34.797 -4.295 -48.565 1 55.32 ? O1A ADP 501 D 1 
HETATM 7 O O2A ADP . . . H 2 36.197 -5.842 -46.993 1 55.32 ? O2A ADP 501 D 1 
HETATM 8 O O3A ADP . . . H 2 37.25 -3.795 -48.086 1 55.32 ? O3A ADP 501 D 1 
HETATM 9 O O5' ADP . . . H 2 35.539 -3.481 -46.262 1 55.32 ? O5' ADP 501 D 1 
HETATM 10 C C5' ADP . . . H 2 35.972 -3.762 -44.928 1 55.32 ? C5' ADP 501 D 1 
HETATM 11 C C4' ADP . . . H 2 34.789 -4.278 -44.121 1 55.32 ? C4' ADP 501 D 1 
HETATM 12 O O4' ADP . . . H 2 35.123 -5.589 -43.649 1 55.32 ? O4' ADP 501 D 1 
HETATM 13 C C3' ADP . . . H 2 34.393 -3.426 -42.91 1 55.32 ? C3' ADP 501 D 1 
HETATM 14 O O3' ADP . . . H 2 33.24 -2.611 -43.175 1 55.32 ? O3' ADP 501 D 1 
HETATM 15 C C2' ADP . . . H 2 34.159 -4.438 -41.789 1 55.32 ? C2' ADP 501 D 1 
HETATM 16 O O2' ADP . . . H 2 32.767 -4.712 -41.538 1 55.32 ? O2' ADP 501 D 1 
HETATM 17 C C1' ADP . . . H 2 34.893 -5.704 -42.244 1 55.32 ? C1' ADP 501 D 1 
HETATM 18 N N9 ADP . . . H 2 36.207 -5.772 -41.55 1 55.32 ? N9 ADP 501 D 1 
HETATM 19 C C8 ADP . . . H 2 37.159 -4.826 -41.693 1 55.32 ? C8 ADP 501 D 1 
HETATM 20 N N7 ADP . . . H 2 38.254 -5.119 -40.946 1 55.32 ? N7 ADP 501 D 1 
HETATM 21 C C5 ADP . . . H 2 38.016 -6.275 -40.305 1 55.32 ? C5 ADP 501 D 1 
HETATM 22 C C6 ADP . . . H 2 38.773 -7.124 -39.354 1 55.32 ? C6 ADP 501 D 1 
HETATM 23 N N6 ADP . . . H 2 40.02 -6.762 -38.961 1 55.32 ? N6 ADP 501 D 1 
HETATM 24 N N1 ADP . . . H 2 38.171 -8.251 -38.912 1 55.32 ? N1 ADP 501 D 1 
HETATM 25 C C2 ADP . . . H 2 36.929 -8.601 -39.309 1 55.32 ? C2 ADP 501 D 1 
HETATM 26 N N3 ADP . . . H 2 36.19 -7.867 -40.169 1 55.32 ? N3 ADP 501 D 1 
HETATM 27 C C4 ADP . . . H 2 36.662 -6.708 -40.696 1 55.32 ? C4 ADP 501 D 1 
HETATM 28 H "H5'1" ADP . . . H 2 36.368 -2.855 -44.468 1 19.86 ? "H5'1" ADP 501 D 1 
HETATM 29 H "H5'2" ADP . . . H 2 36.765 -4.513 -44.946 1 19.86 ? "H5'2" ADP 501 D 1 
HETATM 30 H H4' ADP . . . H 2 33.92 -4.344 -44.791 1 19.86 ? H4' ADP 501 D 1 
HETATM 31 H H3' ADP . . . H 2 35.245 -2.788 -42.635 1 19.86 ? H3' ADP 501 D 1 
HETATM 32 H HO3' ADP . . . H 2 33.025 -2.091 -42.389 1 19.86 ? HO3' ADP 501 D 1 
HETATM 33 H H2' ADP . . . H 2 34.637 -4.065 -40.873 1 19.86 ? H2' ADP 501 D 1 
HETATM 34 H HO2' ADP . . . H 2 32.324 -3.898 -41.263 1 19.86 ? HO2' ADP 501 D 1 
HETATM 35 H H1' ADP . . . H 2 34.282 -6.59 -42.017 1 19.86 ? H1' ADP 501 D 1 
HETATM 36 H H8 ADP . . . H 2 37.063 -3.948 -42.32 1 19.86 ? H8 ADP 501 D 1 
HETATM 37 H HN61 ADP . . . H 2 40.536 -7.346 -38.318 1 19.86 ? HN61 ADP 501 D 1 
HETATM 38 H HN62 ADP . . . H 2 40.436 -5.913 -39.317 1 19.86 ? HN62 ADP 501 D 1 
HETATM 39 H H2 ADP . . . H 2 36.504 -9.516 -38.917 1 19.86 ? H2 ADP 501 D 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           39 
#