data_8F5J
#
_model_server_result.job_id            ifB65zOE3gfHj7rHa7gSdA 
_model_server_result.datetime_utc      '2024-12-26 13:08:14' 
_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          8f5j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    8F5J 
#
_exptl.entry_id    8F5J 
_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            8F5J 
_cell.length_a            132.27 
_cell.length_b            132.27 
_cell.length_c            121.7 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8F5J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        181 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 64 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F 1 1 
A,B,C,D,E,F 1 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' 4_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 66.135 -114.54918 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
metalc ? metalc1 A OD1 ASN 249 A ASN 249 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc2 A O VAL 298 A VAL 298 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? 
metalc ? metalc3 A O ASP 300 A ASP 300 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? 
metalc ? metalc4 A O PHE 303 A PHE 303 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? 
metalc ? metalc5 A O GLY 337 A GLY 337 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? 
metalc ? metalc6 B O1B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc7 B O1A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
metalc ? metalc8 B O2A ADP . A ADP 401 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? 
#
_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                     8F5J 
_atom_sites.fract_transf_matrix[1][1]    0.00756 
_atom_sites.fract_transf_matrix[1][2]    0.004365 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00873 
_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]    0.008217 
_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 1 401 401 ADP ADP . 
C 3 MG A 1 402 402 MG MG . 
D 4 K A 1 403 403 K K . 
E 5 XER A 1 404 501 XER PFE . 
F 6 HOH A 1 501 2 HOH HOH . 
F 6 HOH A 2 502 17 HOH HOH . 
F 6 HOH A 3 503 9 HOH HOH . 
F 6 HOH A 4 504 16 HOH HOH . 
F 6 HOH A 5 505 1 HOH HOH . 
F 6 HOH A 6 506 4 HOH HOH . 
F 6 HOH A 7 507 23 HOH HOH . 
F 6 HOH A 8 508 13 HOH HOH . 
F 6 HOH A 9 509 20 HOH HOH . 
F 6 HOH A 10 510 24 HOH HOH . 
F 6 HOH A 11 511 18 HOH HOH . 
F 6 HOH A 12 512 27 HOH HOH . 
F 6 HOH A 13 513 8 HOH HOH . 
F 6 HOH A 14 514 10 HOH HOH . 
F 6 HOH A 15 515 19 HOH HOH . 
F 6 HOH A 16 516 26 HOH HOH . 
F 6 HOH A 17 517 25 HOH HOH . 
F 6 HOH A 18 518 7 HOH HOH . 
F 6 HOH A 19 519 12 HOH HOH . 
F 6 HOH A 20 520 22 HOH HOH . 
F 6 HOH A 21 521 6 HOH HOH . 
F 6 HOH A 22 522 3 HOH HOH . 
F 6 HOH A 23 523 14 HOH HOH . 
F 6 HOH A 24 524 11 HOH HOH . 
F 6 HOH A 25 525 28 HOH HOH . 
F 6 HOH A 26 526 5 HOH HOH . 
F 6 HOH A 27 527 21 HOH HOH . 
F 6 HOH A 28 528 15 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 27.108 -37.723 13.772 1 100.22 ? PB ADP 401 A 1 
HETATM 2 O O1B ADP . . . B 2 26.416 -38.348 12.516 1 100.38 ? O1B ADP 401 A 1 
HETATM 3 O O2B ADP . . . B 2 26.302 -36.493 14.161 1 100.31 ? O2B ADP 401 A 1 
HETATM 4 O O3B ADP . . . B 2 28.542 -37.382 13.538 1 100.26 ? O3B ADP 401 A 1 
HETATM 5 P PA ADP . . . B 2 27.208 -40.346 15.153 1 98.9 ? PA ADP 401 A 1 
HETATM 6 O O1A ADP . . . B 2 26.321 -41.146 14.274 1 98.94 ? O1A ADP 401 A 1 
HETATM 7 O O2A ADP . . . B 2 26.941 -40.658 16.62 1 98.65 ? O2A ADP 401 A 1 
HETATM 8 O O3A ADP . . . B 2 26.929 -38.783 14.957 1 99.73 ? O3A ADP 401 A 1 
HETATM 9 O O5' ADP . . . B 2 28.761 -40.7 14.896 1 98.6 ? O5' ADP 401 A 1 
HETATM 10 C C5' ADP . . . B 2 29.867 -40.167 15.664 1 98.09 ? C5' ADP 401 A 1 
HETATM 11 C C4' ADP . . . B 2 31.126 -40.221 14.836 1 97.39 ? C4' ADP 401 A 1 
HETATM 12 O O4' ADP . . . B 2 31.4 -41.584 14.45 1 97.07 ? O4' ADP 401 A 1 
HETATM 13 C C3' ADP . . . B 2 31.089 -39.478 13.507 1 96.98 ? C3' ADP 401 A 1 
HETATM 14 O O3' ADP . . . B 2 31.183 -38.064 13.644 1 96.82 ? O3' ADP 401 A 1 
HETATM 15 C C2' ADP . . . B 2 32.254 -40.129 12.756 1 96.85 ? C2' ADP 401 A 1 
HETATM 16 O O2' ADP . . . B 2 33.525 -39.586 13.102 1 96.81 ? O2' ADP 401 A 1 
HETATM 17 C C1' ADP . . . B 2 32.182 -41.58 13.264 1 96.51 ? C1' ADP 401 A 1 
HETATM 18 N N9 ADP . . . B 2 31.636 -42.542 12.306 1 95.44 ? N9 ADP 401 A 1 
HETATM 19 C C8 ADP . . . B 2 30.449 -43.221 12.373 1 94.83 ? C8 ADP 401 A 1 
HETATM 20 N N7 ADP . . . B 2 30.262 -44.071 11.392 1 94.51 ? N7 ADP 401 A 1 
HETATM 21 C C5 ADP . . . B 2 31.406 -43.936 10.618 1 94.53 ? C5 ADP 401 A 1 
HETATM 22 C C6 ADP . . . B 2 31.838 -44.577 9.437 1 94.09 ? C6 ADP 401 A 1 
HETATM 23 N N6 ADP . . . B 2 31.092 -45.435 8.741 1 93.71 ? N6 ADP 401 A 1 
HETATM 24 N N1 ADP . . . B 2 33.063 -44.254 8.961 1 94.16 ? N1 ADP 401 A 1 
HETATM 25 C C2 ADP . . . B 2 33.788 -43.338 9.611 1 94.13 ? C2 ADP 401 A 1 
HETATM 26 N N3 ADP . . . B 2 33.474 -42.648 10.709 1 94.49 ? N3 ADP 401 A 1 
HETATM 27 C C4 ADP . . . B 2 32.262 -42.999 11.17 1 94.95 ? C4 ADP 401 A 1 
#
_model_server_stats.io_time_ms              59 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#