data_8YK9
#
_model_server_result.job_id            Hspj8ukHL7RwI8QT4-YmAQ 
_model_server_result.datetime_utc      '2024-10-13 02:29:55' 
_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          8yk9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":201}' 
#
_entry.id    8YK9 
#
_exptl.entry_id    8YK9 
_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    4 
_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            8YK9 
_cell.length_a            159.233 
_cell.length_b            159.233 
_cell.length_c            127.871 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YK9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,B,E,F,G 1 1 
C,D,H,I 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 E N N 
? 2 F N N 
? 2 H 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
disulf ? disulf1 A SG CYS 88 A CYS 88 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf2 B SG CYS 88 B CYS 88 1_555 B SG CYS 91 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf3 C SG CYS 88 C CYS 88 1_555 C SG CYS 91 C CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf4 D SG CYS 88 D CYS 88 1_555 D SG CYS 91 D CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc1 B OD1 ASP 25 B ASP 25 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? 
metalc ? metalc2 G MG MG . B MG 202 1_555 H O2B ADP . C ADP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? 
#
_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                     8YK9 
_atom_sites.fract_transf_matrix[1][1]    0.00628 
_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]    0.00628 
_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]    0.00782 
_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 1 201 201 ADP ADP . 
F 2 ADP B 1 201 201 ADP ADP . 
G 3 MG B 1 202 202 MG MG . 
H 2 ADP C 1 201 201 ADP ADP . 
I 2 ADP D 1 201 201 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 -48.492 -22.375 16.105 1 156.93 ? PB ADP 201 C 1 
HETATM 2 O O1B ADP . . . H 2 -47.299 -22.893 15.306 1 153.31 -1 O1B ADP 201 C 1 
HETATM 3 O O2B ADP . . . H 2 -49.113 -23.416 17.023 1 140.02 ? O2B ADP 201 C 1 
HETATM 4 O O3B ADP . . . H 2 -49.473 -21.529 15.32 1 139.71 ? O3B ADP 201 C 1 
HETATM 5 P PA ADP . . . H 2 -46.723 -20.223 16.927 1 162.95 ? PA ADP 201 C 1 
HETATM 6 O O1A ADP . . . H 2 -47.233 -18.958 16.235 1 131.42 ? O1A ADP 201 C 1 
HETATM 7 O O2A ADP . . . H 2 -45.57 -20.954 16.257 1 156.6 -1 O2A ADP 201 C 1 
HETATM 8 O O3A ADP . . . H 2 -47.938 -21.273 17.154 1 156.17 ? O3A ADP 201 C 1 
HETATM 9 O O5' ADP . . . H 2 -46.387 -19.984 18.513 1 153.75 ? O5' ADP 201 C 1 
HETATM 10 C C5' ADP . . . H 2 -46.055 -21.1 19.372 1 152.18 ? C5' ADP 201 C 1 
HETATM 11 C C4' ADP . . . H 2 -45.709 -20.785 20.845 1 158.3 ? C4' ADP 201 C 1 
HETATM 12 O O4' ADP . . . H 2 -44.853 -21.819 21.375 1 163.18 ? O4' ADP 201 C 1 
HETATM 13 C C3' ADP . . . H 2 -44.981 -19.462 21.095 1 161.23 ? C3' ADP 201 C 1 
HETATM 14 O O3' ADP . . . H 2 -45.75 -18.613 21.963 1 158.94 ? O3' ADP 201 C 1 
HETATM 15 C C2' ADP . . . H 2 -43.624 -19.826 21.707 1 161.12 ? C2' ADP 201 C 1 
HETATM 16 O O2' ADP . . . H 2 -43.525 -19.407 23.08 1 155.36 ? O2' ADP 201 C 1 
HETATM 17 C C1' ADP . . . H 2 -43.512 -21.344 21.576 1 159.68 ? C1' ADP 201 C 1 
HETATM 18 N N9 ADP . . . H 2 -42.785 -21.682 20.319 1 160.78 ? N9 ADP 201 C 1 
HETATM 19 C C8 ADP . . . H 2 -42.555 -20.79 19.319 1 155.03 ? C8 ADP 201 C 1 
HETATM 20 N N7 ADP . . . H 2 -41.901 -21.341 18.269 1 147.64 ? N7 ADP 201 C 1 
HETATM 21 C C5 ADP . . . H 2 -41.696 -22.629 18.603 1 153.09 ? C5 ADP 201 C 1 
HETATM 22 C C6 ADP . . . H 2 -41.051 -23.756 17.917 1 145.74 ? C6 ADP 201 C 1 
HETATM 23 N N6 ADP . . . H 2 -40.543 -23.509 16.686 1 136.77 ? N6 ADP 201 C 1 
HETATM 24 N N1 ADP . . . H 2 -41.02 -24.956 18.554 1 148.09 ? N1 ADP 201 C 1 
HETATM 25 C C2 ADP . . . H 2 -41.569 -25.117 19.78 1 146.81 ? C2 ADP 201 C 1 
HETATM 26 N N3 ADP . . . H 2 -42.179 -24.13 20.473 1 145.46 ? N3 ADP 201 C 1 
HETATM 27 C C4 ADP . . . H 2 -42.269 -22.873 19.947 1 157.5 ? C4 ADP 201 C 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           267 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#