data_8F5S
#
_model_server_result.job_id            qxYo0FMg4pn4gdz8ZlF1Sw 
_model_server_result.datetime_utc      '2025-01-10 14:19:29' 
_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          8f5s 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":401}' 
#
_entry.id    8F5S 
#
_exptl.entry_id    8F5S 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            8F5S 
_cell.length_a            117.767 
_cell.length_b            117.767 
_cell.length_c            154.773 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8F5S 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        91 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 2 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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_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,I,J,O 1 1 
A,C,D,E,F,G,H,I,J,O 1 3 
B,K,L,M,N,P 2 1 
B,K,L,M,N,P 2 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' 5_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 117.767 0 0 
3 'crystal symmetry operation' 6_545 x,-y-1,-z+1/2 1 0 0 0 -1 0 0 0 -1 0 -117.767 77.3865 
#
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 K 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 OD1 ASN 249 A ASN 249 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? 
metalc ? metalc2 A O VAL 298 A VAL 298 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc3 A O ASP 300 A ASP 300 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.196 ? 
metalc ? metalc4 A O PHE 303 A PHE 303 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.172 ? 
metalc ? metalc5 A O GLY 337 A GLY 337 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.422 ? 
metalc ? metalc6 C O3B ADP . A ADP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc7 C O1A ADP . A ADP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? 
metalc ? metalc8 C O2A ADP . A ADP 401 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? 
metalc ? metalc9 B OD1 ASN 249 B ASN 249 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
metalc ? metalc10 K O1B ADP . B ADP 401 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? 
metalc ? metalc11 K O1A ADP . B ADP 401 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? 
#
_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                     8F5S 
_atom_sites.fract_transf_matrix[1][1]    0.008491 
_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]    0.008491 
_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]    0.006461 
_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 1 401 401 ADP ADP . 
D 3 MG A 1 402 402 MG MG . 
E 4 K A 1 403 403 K K . 
F 5 XGT A 1 404 404 XGT PFE . 
G 6 SO4 A 1 405 1 SO4 SO4 . 
H 6 SO4 A 1 406 2 SO4 SO4 . 
I 6 SO4 A 1 407 4 SO4 SO4 . 
J 6 SO4 A 1 408 5 SO4 SO4 . 
K 2 ADP B 1 401 401 ADP ADP . 
L 3 MG B 1 402 402 MG MG . 
M 5 XGT B 1 403 404 XGT PFE . 
N 6 SO4 B 1 404 6 SO4 SO4 . 
O 7 HOH A 1 501 2 HOH HOH . 
O 7 HOH A 2 502 5 HOH HOH . 
O 7 HOH A 3 503 1 HOH HOH . 
O 7 HOH A 4 504 11 HOH HOH . 
O 7 HOH A 5 505 8 HOH HOH . 
O 7 HOH A 6 506 10 HOH HOH . 
O 7 HOH A 7 507 6 HOH HOH . 
O 7 HOH A 8 508 3 HOH HOH . 
O 7 HOH A 9 509 7 HOH HOH . 
O 7 HOH A 10 510 4 HOH HOH . 
O 7 HOH A 11 511 12 HOH HOH . 
P 7 HOH B 1 501 9 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 . . . K 2 46.76 -88.161 16.372 1 164.84 ? PB ADP 401 B 1 
HETATM 2 O O1B ADP . . . K 2 46.649 -86.892 15.551 1 164.58 ? O1B ADP 401 B 1 
HETATM 3 O O2B ADP . . . K 2 45.439 -88.584 16.982 1 164.94 ? O2B ADP 401 B 1 
HETATM 4 O O3B ADP . . . K 2 47.888 -88.119 17.377 1 164.84 ? O3B ADP 401 B 1 
HETATM 5 P PA ADP . . . K 2 47.719 -89.468 13.852 1 165 ? PA ADP 401 B 1 
HETATM 6 O O1A ADP . . . K 2 47.23 -88.311 13.066 1 165.06 ? O1A ADP 401 B 1 
HETATM 7 O O2A ADP . . . K 2 47.485 -90.85 13.364 1 165 ? O2A ADP 401 B 1 
HETATM 8 O O3A ADP . . . K 2 47.148 -89.345 15.34 1 164.93 ? O3A ADP 401 B 1 
HETATM 9 O O5' ADP . . . K 2 49.284 -89.287 14.094 1 164.6 ? O5' ADP 401 B 1 
HETATM 10 C C5' ADP . . . K 2 50.002 -90.202 14.949 1 164.23 ? C5' ADP 401 B 1 
HETATM 11 C C4' ADP . . . K 2 51.271 -89.518 15.385 1 163.83 ? C4' ADP 401 B 1 
HETATM 12 O O4' ADP . . . K 2 52.053 -89.169 14.224 1 163.43 ? O4' ADP 401 B 1 
HETATM 13 C C3' ADP . . . K 2 51.051 -88.19 16.089 1 164.08 ? C3' ADP 401 B 1 
HETATM 14 O O3' ADP . . . K 2 50.723 -88.379 17.459 1 164.26 ? O3' ADP 401 B 1 
HETATM 15 C C2' ADP . . . K 2 52.391 -87.481 15.875 1 164 ? C2' ADP 401 B 1 
HETATM 16 O O2' ADP . . . K 2 53.36 -87.801 16.868 1 164.15 ? O2' ADP 401 B 1 
HETATM 17 C C1' ADP . . . K 2 52.828 -88.013 14.504 1 163.65 ? C1' ADP 401 B 1 
HETATM 18 N N9 ADP . . . K 2 52.667 -87.05 13.418 1 163.57 ? N9 ADP 401 B 1 
HETATM 19 C C8 ADP . . . K 2 51.662 -86.994 12.487 1 163.3 ? C8 ADP 401 B 1 
HETATM 20 N N7 ADP . . . K 2 51.76 -85.986 11.653 1 163.32 ? N7 ADP 401 B 1 
HETATM 21 C C5 ADP . . . K 2 52.913 -85.331 12.064 1 163.61 ? C5 ADP 401 B 1 
HETATM 22 C C6 ADP . . . K 2 53.581 -84.186 11.581 1 163.77 ? C6 ADP 401 B 1 
HETATM 23 N N6 ADP . . . K 2 53.142 -83.437 10.563 1 163.96 ? N6 ADP 401 B 1 
HETATM 24 N N1 ADP . . . K 2 54.716 -83.811 12.207 1 163.7 ? N1 ADP 401 B 1 
HETATM 25 C C2 ADP . . . K 2 55.143 -84.532 13.248 1 163.72 ? C2 ADP 401 B 1 
HETATM 26 N N3 ADP . . . K 2 54.599 -85.623 13.792 1 163.7 ? N3 ADP 401 B 1 
HETATM 27 C C4 ADP . . . K 2 53.481 -85.975 13.151 1 163.65 ? C4 ADP 401 B 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           343 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           27 
#