data_5M3E
#
_model_server_result.job_id            Wu3E4L9GwA8YrAme_WnBeA 
_model_server_result.datetime_utc      '2025-01-07 13:02:50' 
_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          5m3e 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    5M3E 
#
_exptl.entry_id    5M3E 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          2 
_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            5M3E 
_cell.length_a            37.41 
_cell.length_b            60.392 
_cell.length_c            76.706 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5M3E 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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                     5M3E 
_atom_sites.fract_transf_matrix[1][1]    0.026731 
_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]    0.016558 
_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]    0.013037 
_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 APR A 1 201 1 APR APR . 
C 3 CL A 1 202 1 CL CL . 
D 4 HOH A 1 301 5 HOH HOH . 
D 4 HOH A 2 302 15 HOH HOH . 
D 4 HOH A 3 303 16 HOH HOH . 
D 4 HOH A 4 304 1 HOH HOH . 
D 4 HOH A 5 305 11 HOH HOH . 
D 4 HOH A 6 306 3 HOH HOH . 
D 4 HOH A 7 307 4 HOH HOH . 
D 4 HOH A 8 308 2 HOH HOH . 
D 4 HOH A 9 309 14 HOH HOH . 
D 4 HOH A 10 310 7 HOH HOH . 
D 4 HOH A 11 311 6 HOH HOH . 
D 4 HOH A 12 312 8 HOH HOH . 
D 4 HOH A 13 313 17 HOH HOH . 
D 4 HOH A 14 314 13 HOH HOH . 
D 4 HOH A 15 315 10 HOH HOH . 
D 4 HOH A 16 316 12 HOH HOH . 
D 4 HOH A 17 317 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 N N1 APR . . . B 2 -5.758 -4.984 23.172 1 44.62 ? N1 APR 201 A 1 
HETATM 2 C C2 APR . . . B 2 -6.312 -6.209 23.32 1 44.98 ? C2 APR 201 A 1 
HETATM 3 N N3 APR . . . B 2 -7.585 -6.396 23.722 1 44.67 ? N3 APR 201 A 1 
HETATM 4 C C4 APR . . . B 2 -8.38 -5.336 24.008 1 43.84 ? C4 APR 201 A 1 
HETATM 5 C C5 APR . . . B 2 -7.858 -3.96 23.872 1 44.38 ? C5 APR 201 A 1 
HETATM 6 C C6 APR . . . B 2 -6.451 -3.849 23.42 1 44.69 ? C6 APR 201 A 1 
HETATM 7 N N6 APR . . . B 2 -5.859 -2.649 23.26 1 47.09 ? N6 APR 201 A 1 
HETATM 8 N N7 APR . . . B 2 -8.86 -3.117 24.213 1 42.52 ? N7 APR 201 A 1 
HETATM 9 C C8 APR . . . B 2 -9.936 -3.891 24.533 1 44.57 ? C8 APR 201 A 1 
HETATM 10 N N9 APR . . . B 2 -9.632 -5.215 24.417 1 43.76 ? N9 APR 201 A 1 
HETATM 11 C C1' APR . . . B 2 -10.495 -6.395 24.634 1 43.29 ? C1' APR 201 A 1 
HETATM 12 C C2' APR . . . B 2 -11.521 -6.253 25.743 1 42.14 ? C2' APR 201 A 1 
HETATM 13 O O2' APR . . . B 2 -11.505 -7.451 26.518 1 47.31 ? O2' APR 201 A 1 
HETATM 14 C C3' APR . . . B 2 -12.849 -6.147 25.046 1 42.41 ? C3' APR 201 A 1 
HETATM 15 O O3' APR . . . B 2 -13.915 -6.728 25.825 1 42.46 ? O3' APR 201 A 1 
HETATM 16 O O4' APR . . . B 2 -11.216 -6.603 23.413 1 41.3 ? O4' APR 201 A 1 
HETATM 17 C C4' APR . . . B 2 -12.575 -6.883 23.728 1 40.76 ? C4' APR 201 A 1 
HETATM 18 C C5' APR . . . B 2 -13.462 -6.514 22.545 1 38.18 ? C5' APR 201 A 1 
HETATM 19 O O5' APR . . . B 2 -13.593 -5.09 22.414 1 37.46 ? O5' APR 201 A 1 
HETATM 20 P PA APR . . . B 2 -14.967 -4.466 21.854 1 34.55 ? PA APR 201 A 1 
HETATM 21 O O1A APR . . . B 2 -14.597 -3.122 21.294 1 36.29 ? O1A APR 201 A 1 
HETATM 22 O O2A APR . . . B 2 -16.029 -4.592 22.909 1 32.96 ? O2A APR 201 A 1 
HETATM 23 O O3A APR . . . B 2 -15.305 -5.427 20.577 1 33.6 ? O3A APR 201 A 1 
HETATM 24 P PB APR . . . B 2 -16.715 -6.161 20.259 1 33.73 ? PB APR 201 A 1 
HETATM 25 O O1B APR . . . B 2 -17.205 -6.882 21.486 1 31.87 ? O1B APR 201 A 1 
HETATM 26 O O2B APR . . . B 2 -16.579 -6.95 18.955 1 34.99 ? O2B APR 201 A 1 
HETATM 27 O O5D APR . . . B 2 -17.763 -4.977 19.959 1 35.21 ? O5D APR 201 A 1 
HETATM 28 C C5D APR . . . B 2 -17.898 -4.296 18.704 1 33.61 ? C5D APR 201 A 1 
HETATM 29 O O4D APR . . . B 2 -17.615 -2.2 19.896 1 34.31 ? O4D APR 201 A 1 
HETATM 30 O O1D APR . . . B 2 -15.402 -1.813 19.306 1 34.43 ? O1D APR 201 A 1 
HETATM 31 C C1D APR . . . B 2 -16.741 -1.316 19.198 1 33.99 ? C1D APR 201 A 1 
HETATM 32 O O2D APR . . . B 2 -17.234 0.048 17.24 1 33.16 ? O2D APR 201 A 1 
HETATM 33 C C2D APR . . . B 2 -17.174 -1.294 17.735 1 34.27 ? C2D APR 201 A 1 
HETATM 34 O O3D APR . . . B 2 -19.618 -1.155 17.684 1 34.09 ? O3D APR 201 A 1 
HETATM 35 C C3D APR . . . B 2 -18.493 -2.043 17.689 1 33.75 ? C3D APR 201 A 1 
HETATM 36 C C4D APR . . . B 2 -18.454 -2.889 18.956 1 34.28 ? C4D APR 201 A 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           53 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           562 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           36 
#