data_8E6V
#
_model_server_result.job_id            '_BHQw4NedERGIXlej0Harw' 
_model_server_result.datetime_utc      '2024-11-15 15:00:24' 
_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          8e6v 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1602}' 
#
_entry.id    8E6V 
#
_exptl.entry_id    8E6V 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    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            8E6V 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8E6V 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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    ? 
_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 B N N 
? 2 C 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 SG CYS 72 A CYS 72 1_555 D ZN ZN . A ZN 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? 
metalc ? metalc2 A SG CYS 89 A CYS 89 1_555 D ZN ZN . A ZN 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc3 A SG CYS 91 A CYS 91 1_555 D ZN ZN . A ZN 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc4 A NE2 HIS 98 A HIS 98 1_555 D ZN ZN . A ZN 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
#
_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                     8E6V 
_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
B 2 APR A 1 1601 1601 APR APR . 
C 2 APR A 1 1602 1602 APR APR . 
D 3 ZN A 1 1603 1603 ZN ZN . 
#
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 2 171.404 195.869 262.132 1 77.25 ? N1 APR 1602 A 1 
HETATM 2 C C2 APR . . . C 2 171.338 197.169 261.818 1 77.25 ? C2 APR 1602 A 1 
HETATM 3 N N3 APR . . . C 2 170.419 198.071 262.151 1 77.25 ? N3 APR 1602 A 1 
HETATM 4 C C4 APR . . . C 2 169.462 197.512 262.908 1 77.25 ? C4 APR 1602 A 1 
HETATM 5 C C5 APR . . . C 2 169.39 196.198 263.316 1 77.25 ? C5 APR 1602 A 1 
HETATM 6 C C6 APR . . . C 2 170.423 195.337 262.9 1 77.25 ? C6 APR 1602 A 1 
HETATM 7 N N6 APR . . . C 2 170.482 194.047 263.217 1 77.25 ? N6 APR 1602 A 1 
HETATM 8 N N7 APR . . . C 2 168.252 195.998 264.088 1 77.25 ? N7 APR 1602 A 1 
HETATM 9 C C8 APR . . . C 2 167.669 197.174 264.132 1 77.25 ? C8 APR 1602 A 1 
HETATM 10 N N9 APR . . . C 2 168.361 198.132 263.434 1 77.25 ? N9 APR 1602 A 1 
HETATM 11 C C1' APR . . . C 2 168.011 199.535 263.265 1 77.25 ? C1' APR 1602 A 1 
HETATM 12 C C2' APR . . . C 2 167.135 199.829 262.053 1 77.25 ? C2' APR 1602 A 1 
HETATM 13 C C3' APR . . . C 2 166.527 201.162 262.493 1 77.25 ? C3' APR 1602 A 1 
HETATM 14 O O3' APR . . . C 2 167.492 202.195 262.34 1 77.25 ? O3' APR 1602 A 1 
HETATM 15 O O4' APR . . . C 2 167.262 199.948 264.386 1 77.25 ? O4' APR 1602 A 1 
HETATM 16 C C4' APR . . . C 2 166.243 200.898 263.977 1 77.25 ? C4' APR 1602 A 1 
HETATM 17 C C5' APR . . . C 2 164.891 200.305 264.289 1 77.25 ? C5' APR 1602 A 1 
HETATM 18 O O5' APR . . . C 2 164.59 200.507 265.693 1 77.25 ? O5' APR 1602 A 1 
HETATM 19 P PA APR . . . C 2 163.194 199.959 266.262 1 77.25 ? PA APR 1602 A 1 
HETATM 20 O O1A APR . . . C 2 162.11 200.259 265.281 1 77.25 ? O1A APR 1602 A 1 
HETATM 21 O O2A APR . . . C 2 163.014 200.437 267.665 1 77.25 ? O2A APR 1602 A 1 
HETATM 22 O O3A APR . . . C 2 163.46 198.378 266.294 1 77.25 ? O3A APR 1602 A 1 
HETATM 23 P PB APR . . . C 2 164.463 197.479 267.165 1 77.25 ? PB APR 1602 A 1 
HETATM 24 O O1B APR . . . C 2 164.222 196.032 266.515 1 77.25 ? O1B APR 1602 A 1 
HETATM 25 O O2B APR . . . C 2 163.988 197.47 268.58 1 77.25 ? O2B APR 1602 A 1 
HETATM 26 O O5D APR . . . C 2 165.863 197.917 266.891 1 77.25 ? O5D APR 1602 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           371 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#