data_2P8X
#
_model_server_result.job_id            0n9Q8H2HPNiCzAQT2LI6Zg 
_model_server_result.datetime_utc      '2025-07-03 21:57:16' 
_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          2p8x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1699}' 
#
_entry.id    2P8X 
#
_exptl.entry_id    2P8X 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ADENOSINE-5-DIPHOSPHORIBOSE 
_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         90 
_cell.entry_id            2P8X 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2P8X 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1' 
#
_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 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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
covale ? covale1 A CG2 ILE 698 T ILE 698 1_555 A CG DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
covale ? covale2 A CA ILE 698 T ILE 698 1_555 A ND1 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
covale ? covale3 A CG2 ILE 698 T ILE 698 1_555 A CAT DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.695 ? 
covale ? covale4 A CB ILE 698 T ILE 698 1_555 A CAT DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? 
covale ? covale5 A CG2 ILE 698 T ILE 698 1_555 A NE2 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? 
covale ? covale6 A CB ILE 698 T ILE 698 1_555 A CE1 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.7 ? 
covale ? covale7 A CG2 ILE 698 T ILE 698 1_555 A ND1 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.068 ? 
covale ? covale8 A CB ILE 698 T ILE 698 1_555 A ND1 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.529 ? 
covale ? covale9 A C ILE 698 T ILE 698 1_555 A ND1 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
covale ? covale10 A C DDE 699 T DDE 699 1_555 A N ARG 700 T ARG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? 
covale ? covale11 A NE2 DDE 699 T DDE 699 1_555 C C1D APR . T APR 1699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? 
#
_chem_comp.formula           'C15 H23 N5 O14 P2' 
_chem_comp.formula_weight    559.316 
_chem_comp.id                APR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ADENOSINE-5-DIPHOSPHORIBOSE 
_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
N1 C2 APR sing 13 n y 
N1 C6 APR doub 14 n y 
C2 N3 APR doub 15 n y 
C2 H2 APR sing 16 n n 
N3 C4 APR sing 17 n y 
C4 C5 APR doub 18 n y 
C4 N9 APR sing 19 n y 
C5 C6 APR sing 20 n y 
C5 N7 APR sing 21 n y 
C6 N6 APR sing 22 n n 
N6 H61 APR sing 23 n n 
N6 H62 APR sing 24 n n 
N7 C8 APR doub 25 n y 
C8 N9 APR sing 26 n y 
C8 H8 APR sing 27 n n 
N9 C1' APR sing 28 n n 
C1' C2' APR sing 29 n n 
C1' O4' APR sing 30 n n 
C1' "H'1" APR sing 31 n n 
C2' O2' APR sing 32 n n 
C2' C3' APR sing 33 n n 
C2' "H'2" APR sing 34 n n 
O2' "HO'2" APR sing 35 n n 
C3' O3' APR sing 36 n n 
C3' C4' APR sing 37 n n 
C3' "H'3" APR sing 38 n n 
O3' "HO'3" APR sing 39 n n 
O4' C4' APR sing 40 n n 
C4' C5' APR sing 41 n n 
C4' "H'4" APR sing 42 n n 
C5' O5' APR sing 43 n n 
C5' "H5'1" APR sing 44 n n 
C5' "H5'2" APR sing 45 n n 
O5' PA APR sing 46 n n 
PA O1A APR doub 47 n n 
PA O2A APR sing 48 n n 
PA O3A APR sing 49 n n 
O2A HOA2 APR sing 50 n n 
O3A PB APR sing 51 n n 
PB O1B APR doub 52 n n 
PB O2B APR sing 53 n n 
PB O5D APR sing 54 n n 
O2B HOB2 APR sing 55 n n 
O5D C5D APR sing 56 n n 
C5D C4D APR sing 57 n n 
C5D H5R1 APR sing 58 n n 
C5D H5R2 APR sing 59 n n 
O4D C1D APR sing 60 n n 
O4D C4D APR sing 61 n n 
O1D C1D APR sing 62 n n 
O1D HOR1 APR sing 63 n n 
C1D C2D APR sing 64 n n 
C1D "HR'1" APR sing 65 n n 
O2D C2D APR sing 66 n n 
O2D HOR2 APR sing 67 n n 
C2D C3D APR sing 68 n n 
C2D "HR'2" APR sing 69 n n 
O3D C3D APR sing 70 n n 
O3D HOR3 APR sing 71 n n 
C3D C4D APR sing 72 n n 
C3D "HR'3" APR sing 73 n n 
C4D "HR'4" APR sing 74 n n 
#
_atom_sites.entry_id                     2P8X 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 3 APR T 1 1699 1699 APR APR . 
D 4 GNP T 1 843 843 GNP GNP . 
#
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 N N1 APR . . . C 3 -54.162 7.146 5.894 1 128.4 ? N1 APR 1699 T 1 
HETATM 2 C C2 APR . . . C 3 -53.773 8.43 6.298 1 128.31 ? C2 APR 1699 T 1 
HETATM 3 N N3 APR . . . C 3 -54.307 9.574 5.967 1 128.37 ? N3 APR 1699 T 1 
HETATM 4 C C4 APR . . . C 3 -55.37 9.4 5.145 1 128.37 ? C4 APR 1699 T 1 
HETATM 5 C C5 APR . . . C 3 -55.894 8.192 4.665 1 128.39 ? C5 APR 1699 T 1 
HETATM 6 C C6 APR . . . C 3 -55.249 7 5.065 1 128.26 ? C6 APR 1699 T 1 
HETATM 7 N N6 APR . . . C 3 -55.61 5.783 4.67 1 127.85 ? N6 APR 1699 T 1 
HETATM 8 N N7 APR . . . C 3 -57.002 8.408 3.852 1 128.13 ? N7 APR 1699 T 1 
HETATM 9 C C8 APR . . . C 3 -57.118 9.727 3.829 1 128.04 ? C8 APR 1699 T 1 
HETATM 10 N N9 APR . . . C 3 -56.146 10.363 4.575 1 127.95 ? N9 APR 1699 T 1 
HETATM 11 C C1' APR . . . C 3 -55.88 11.788 4.8 1 49.13 ? C1' APR 1699 T 1 
HETATM 12 C C2' APR . . . C 3 -56.169 12.471 3.49 1 48.98 ? C2' APR 1699 T 1 
HETATM 13 O O2' APR . . . C 3 -54.957 12.807 2.809 1 125.61 ? O2' APR 1699 T 1 
HETATM 14 C C3' APR . . . C 3 -57.082 13.673 3.807 1 48.88 ? C3' APR 1699 T 1 
HETATM 15 O O3' APR . . . C 3 -56.419 14.961 3.736 1 125.67 ? O3' APR 1699 T 1 
HETATM 16 O O4' APR . . . C 3 -56.75 12.279 5.773 1 125.97 ? O4' APR 1699 T 1 
HETATM 17 C C4' APR . . . C 3 -57.635 13.363 5.224 1 48.88 ? C4' APR 1699 T 1 
HETATM 18 C C5' APR . . . C 3 -58.758 12.348 5.066 1 48.89 ? C5' APR 1699 T 1 
HETATM 19 O O5' APR . . . C 3 -59.916 12.667 5.008 1 124.22 ? O5' APR 1699 T 1 
HETATM 20 P PA APR . . . C 3 -60.878 11.413 5.297 1 123.75 ? PA APR 1699 T 1 
HETATM 21 O O1A APR . . . C 3 -62.323 11.876 5.251 1 124.17 ? O1A APR 1699 T 1 
HETATM 22 O O2A APR . . . C 3 -60.491 10.898 6.541 1 123.78 ? O2A APR 1699 T 1 
HETATM 23 O O3A APR . . . C 3 -60.849 10.415 4.021 1 120.27 ? O3A APR 1699 T 1 
HETATM 24 P PB APR . . . C 3 -61.655 10.903 2.652 1 117.29 ? PB APR 1699 T 1 
HETATM 25 O O1B APR . . . C 3 -63.128 10.781 2.429 1 117.82 ? O1B APR 1699 T 1 
HETATM 26 O O2B APR . . . C 3 -61.329 12.283 2.613 1 117.53 ? O2B APR 1699 T 1 
HETATM 27 O O5D APR . . . C 3 -60.767 10.265 1.564 1 113.18 ? O5D APR 1699 T 1 
HETATM 28 C C5D APR . . . C 3 -59.445 9.909 1.753 1 48.82 ? C5D APR 1699 T 1 
HETATM 29 O O4D APR . . . C 3 -58.308 11.065 0.201 1 95.21 ? O4D APR 1699 T 1 
HETATM 30 C C1D APR . . . C 3 -56.868 11.208 0.107 1 48.85 ? C1D APR 1699 T 1 
HETATM 31 O O2D APR . . . C 3 -55.353 9.218 -0.168 1 95.95 ? O2D APR 1699 T 1 
HETATM 32 C C2D APR . . . C 3 -56.395 9.829 0.613 1 48.8 ? C2D APR 1699 T 1 
HETATM 33 O O3D APR . . . C 3 -57.406 7.9 -0.58 1 98.4 ? O3D APR 1699 T 1 
HETATM 34 C C3D APR . . . C 3 -57.572 8.858 0.489 1 48.76 ? C3D APR 1699 T 1 
HETATM 35 C C4D APR . . . C 3 -58.804 9.699 0.43 1 48.77 ? C4D APR 1699 T 1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           35 
#