data_8XJ6
#
_model_server_result.job_id            uD_Assyxmb2hc8H1GTY1FA 
_model_server_result.datetime_utc      '2024-11-22 21:42:04' 
_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          8xj6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":801}' 
#
_entry.id    8XJ6 
#
_exptl.entry_id    8XJ6 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              426.216 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'AMP PHOSPHORAMIDATE' 
_entity.pdbx_number_of_molecules    3 
_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            8XJ6 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XJ6 
_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    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,E,F,G,H,I,J,K,L,M,N 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 H N N 
? 3 K N N 
? 3 M 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 E SG CYS 282 E CYS 282 1_555 L ZN ZN . E ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? 
metalc ? metalc2 E SG CYS 285 E CYS 285 1_555 L ZN ZN . E ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc3 E ND1 HIS 290 E HIS 290 1_555 L ZN ZN . E ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? 
metalc ? metalc4 E SG CYS 314 E CYS 314 1_555 L ZN ZN . E ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? 
metalc ? metalc5 F SG CYS 282 F CYS 282 1_555 N ZN ZN . F ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc6 F SG CYS 285 F CYS 285 1_555 N ZN ZN . F ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? 
metalc ? metalc7 F SG CYS 314 F CYS 314 1_555 N ZN ZN . F ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
#
_chem_comp.formula           'C10 H16 N6 O9 P2' 
_chem_comp.formula_weight    426.216 
_chem_comp.id                AN2 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'AMP PHOSPHORAMIDATE' 
_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
N3B PB AN2 sing 13 n n 
N3B H3B1 AN2 sing 14 n n 
N3B H3B2 AN2 sing 15 n n 
PB O2B AN2 sing 16 n n 
PB O1B AN2 doub 17 n n 
PB O3A AN2 sing 18 n n 
O2B HO2B AN2 sing 19 n n 
O3A PA AN2 sing 20 n n 
PA O1A AN2 doub 21 n n 
PA O2A AN2 sing 22 n n 
PA O5' AN2 sing 23 n n 
O2A HO2A AN2 sing 24 n n 
O5' C5' AN2 sing 25 n n 
C5' C4' AN2 sing 26 n n 
C5' "H5'1" AN2 sing 27 n n 
C5' "H5'2" AN2 sing 28 n n 
C4' O4' AN2 sing 29 n n 
C4' C3' AN2 sing 30 n n 
C4' H4' AN2 sing 31 n n 
O4' C1' AN2 sing 32 n n 
C3' O3' AN2 sing 33 n n 
C3' C2' AN2 sing 34 n n 
C3' H3' AN2 sing 35 n n 
O3' HA AN2 sing 36 n n 
C2' O2' AN2 sing 37 n n 
C2' C1' AN2 sing 38 n n 
C2' H2' AN2 sing 39 n n 
O2' HB AN2 sing 40 n n 
C1' N9 AN2 sing 41 n n 
C1' H1' AN2 sing 42 n n 
N9 C8 AN2 sing 43 n y 
N9 C4 AN2 sing 44 n y 
C8 N7 AN2 doub 45 n y 
C8 H8 AN2 sing 46 n n 
N7 C5 AN2 sing 47 n y 
C5 C4 AN2 doub 48 n y 
C5 C6 AN2 sing 49 n y 
C4 N3 AN2 sing 50 n y 
N3 C2 AN2 doub 51 n y 
C2 N1 AN2 sing 52 n y 
C2 H2 AN2 sing 53 n n 
N1 C6 AN2 doub 54 n y 
C6 N6 AN2 sing 55 n n 
N6 H6N1 AN2 sing 56 n n 
N6 H6N2 AN2 sing 57 n n 
#
_atom_sites.entry_id                     8XJ6 
_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
G 2 ANP A 1 801 801 ANP ANP . 
H 3 AN2 B 1 801 801 AN2 ANP . 
I 2 ANP C 1 801 801 ANP ANP . 
J 2 ANP D 1 801 801 ANP ANP . 
K 3 AN2 E 1 801 801 AN2 ANP . 
L 4 ZN E 1 802 1 ZN ZN . 
M 3 AN2 F 1 801 801 AN2 ANP . 
N 4 ZN F 1 802 2 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 N3B AN2 . . . M 3 186.583 132.751 179.419 1 161.61 ? N3B AN2 801 F 1 
HETATM 2 P PB AN2 . . . M 3 187.389 131.894 178.351 1 161.61 ? PB AN2 801 F 1 
HETATM 3 O O2B AN2 . . . M 3 187.683 130.53 178.834 1 161.61 ? O2B AN2 801 F 1 
HETATM 4 O O1B AN2 . . . M 3 186.617 131.97 177.035 1 161.61 ? O1B AN2 801 F 1 
HETATM 5 O O3A AN2 . . . M 3 188.707 132.767 178.172 1 161.61 ? O3A AN2 801 F 1 
HETATM 6 P PA AN2 . . . M 3 189.113 134.098 177.415 1 161.61 ? PA AN2 801 F 1 
HETATM 7 O O1A AN2 . . . M 3 188.98 133.815 175.921 1 161.61 ? O1A AN2 801 F 1 
HETATM 8 O O2A AN2 . . . M 3 188.341 135.256 177.908 1 161.61 ? O2A AN2 801 F 1 
HETATM 9 O O5' AN2 . . . M 3 190.647 134.252 177.754 1 161.61 ? O5' AN2 801 F 1 
HETATM 10 C C5' AN2 . . . M 3 191.109 134.301 179.119 1 161.61 ? C5' AN2 801 F 1 
HETATM 11 C C4' AN2 . . . M 3 192.188 135.348 179.242 1 161.61 ? C4' AN2 801 F 1 
HETATM 12 O O4' AN2 . . . M 3 193.473 134.76 178.944 1 161.61 ? O4' AN2 801 F 1 
HETATM 13 C C3' AN2 . . . M 3 192.042 136.565 178.327 1 161.61 ? C3' AN2 801 F 1 
HETATM 14 O O3' AN2 . . . M 3 192.372 137.764 179.017 1 161.61 ? O3' AN2 801 F 1 
HETATM 15 C C2' AN2 . . . M 3 193.027 136.27 177.193 1 161.61 ? C2' AN2 801 F 1 
HETATM 16 O O2' AN2 . . . M 3 193.561 137.464 176.633 1 161.61 ? O2' AN2 801 F 1 
HETATM 17 C C1' AN2 . . . M 3 194.12 135.49 177.922 1 161.61 ? C1' AN2 801 F 1 
HETATM 18 N N9 AN2 . . . M 3 194.834 134.543 177.074 1 161.61 ? N9 AN2 801 F 1 
HETATM 19 C C8 AN2 . . . M 3 194.287 133.534 176.326 1 161.61 ? C8 AN2 801 F 1 
HETATM 20 N N7 AN2 . . . M 3 195.164 132.828 175.655 1 161.61 ? N7 AN2 801 F 1 
HETATM 21 C C5 AN2 . . . M 3 196.377 133.412 175.988 1 161.61 ? C5 AN2 801 F 1 
HETATM 22 C C4 AN2 . . . M 3 196.189 134.471 176.861 1 161.61 ? C4 AN2 801 F 1 
HETATM 23 N N3 AN2 . . . M 3 197.137 135.254 177.382 1 161.61 ? N3 AN2 801 F 1 
HETATM 24 C C2 AN2 . . . M 3 198.349 134.893 176.954 1 161.61 ? C2 AN2 801 F 1 
HETATM 25 N N1 AN2 . . . M 3 198.682 133.905 176.119 1 161.61 ? N1 AN2 801 F 1 
HETATM 26 C C6 AN2 . . . M 3 197.702 133.129 175.607 1 161.61 ? C6 AN2 801 F 1 
HETATM 27 N N6 AN2 . . . M 3 198.043 132.142 174.773 1 161.61 ? N6 AN2 801 F 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#