data_8RKD
#
_model_server_result.job_id            N8RyLScRs8D7PiQuODmNCw 
_model_server_result.datetime_utc      '2024-10-13 19:24:06' 
_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          8rkd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":601}' 
#
_entry.id    8RKD 
#
_exptl.entry_id    8RKD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              506.196 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' 
_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            8RKD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8RKD 
_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,O,P,Q,R 
_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
? 5 L N N 
? 5 R 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 B OG1 THR 209 F THR 288 1_555 K MG MG . F MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc2 J O2B ADP . F ADP 702 1_555 K MG MG . F MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? 
metalc ? metalc3 E OG1 THR 209 C THR 288 1_555 Q MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc4 P O2B ADP . C ADP 702 1_555 Q MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
#
_chem_comp.formula           'C10 H17 N6 O12 P3' 
_chem_comp.formula_weight    506.196 
_chem_comp.id                ANP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' 
_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
PG O1G ANP doub 57 n n 
PG O2G ANP sing 58 n n 
PG O3G ANP sing 59 n n 
PG N3B ANP sing 60 n n 
O2G HOG2 ANP sing 61 n n 
O3G HOG3 ANP sing 62 n n 
PB O1B ANP doub 63 n n 
PB O2B ANP sing 64 n n 
PB N3B ANP sing 65 n n 
PB O3A ANP sing 66 n n 
O2B HOB2 ANP sing 67 n n 
N3B HNB1 ANP sing 68 n n 
PA O1A ANP doub 69 n n 
PA O2A ANP sing 70 n n 
PA O3A ANP sing 71 n n 
PA O5' ANP sing 72 n n 
O2A HOA2 ANP sing 73 n n 
O5' C5' ANP sing 74 n n 
C5' C4' ANP sing 75 n n 
C5' "H5'1" ANP sing 76 n n 
C5' "H5'2" ANP sing 77 n n 
C4' O4' ANP sing 78 n n 
C4' C3' ANP sing 79 n n 
C4' H4' ANP sing 80 n n 
O4' C1' ANP sing 81 n n 
C3' O3' ANP sing 82 n n 
C3' C2' ANP sing 83 n n 
C3' H3' ANP sing 84 n n 
O3' HO3' ANP sing 85 n n 
C2' O2' ANP sing 86 n n 
C2' C1' ANP sing 87 n n 
C2' H2' ANP sing 88 n n 
O2' HO2' ANP sing 89 n n 
C1' N9 ANP sing 90 n n 
C1' H1' ANP sing 91 n n 
N9 C8 ANP sing 92 n y 
N9 C4 ANP sing 93 n y 
C8 N7 ANP doub 94 n y 
C8 H8 ANP sing 95 n n 
N7 C5 ANP sing 96 n y 
C5 C6 ANP sing 97 n y 
C5 C4 ANP doub 98 n y 
C6 N6 ANP sing 99 n n 
C6 N1 ANP doub 100 n y 
N6 HN61 ANP sing 101 n n 
N6 HN62 ANP sing 102 n n 
N1 C2 ANP sing 103 n y 
C2 N3 ANP doub 104 n y 
C2 H2 ANP sing 105 n n 
N3 C4 ANP sing 106 n y 
#
_atom_sites.entry_id                     8RKD 
_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 ADP E 1 601 601 ADP ADP . 
H 3 EPE E 1 602 701 EPE EPE . 
I 3 EPE F 1 701 701 EPE EPE . 
J 2 ADP F 1 702 601 ADP ADP . 
K 4 MG F 1 703 801 MG MG . 
L 5 ANP A 1 601 601 ANP ANP . 
M 3 EPE B 1 701 701 EPE EPE . 
N 2 ADP B 1 702 601 ADP ADP . 
O 3 EPE C 1 701 701 EPE EPE . 
P 2 ADP C 1 702 601 ADP ADP . 
Q 4 MG C 1 703 801 MG MG . 
R 5 ANP D 1 601 601 ANP ANP . 
#
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 PG ANP . . . L 5 170.046 201.971 159.319 1 20 ? PG ANP 601 A 1 
HETATM 2 O O1G ANP . . . L 5 170.446 201.68 157.873 1 20 ? O1G ANP 601 A 1 
HETATM 3 O O2G ANP . . . L 5 171.019 201.438 160.372 1 20 ? O2G ANP 601 A 1 
HETATM 4 O O3G ANP . . . L 5 168.575 201.695 159.622 1 20 ? O3G ANP 601 A 1 
HETATM 5 P PB ANP . . . L 5 169.004 204.86 159.469 1 20 ? PB ANP 601 A 1 
HETATM 6 O O1B ANP . . . L 5 168.716 205.239 158.047 1 20 ? O1B ANP 601 A 1 
HETATM 7 O O2B ANP . . . L 5 167.872 204.537 160.408 1 20 ? O2B ANP 601 A 1 
HETATM 8 N N3B ANP . . . L 5 170.229 203.737 159.553 1 20 ? N3B ANP 601 A 1 
HETATM 9 P PA ANP . . . L 5 169.608 207.719 159.468 1 20 ? PA ANP 601 A 1 
HETATM 10 O O1A ANP . . . L 5 170.848 208.174 158.775 1 20 ? O1A ANP 601 A 1 
HETATM 11 O O2A ANP . . . L 5 168.263 207.826 158.779 1 20 ? O2A ANP 601 A 1 
HETATM 12 O O3A ANP . . . L 5 169.745 206.247 160.104 1 20 ? O3A ANP 601 A 1 
HETATM 13 O O5' ANP . . . L 5 169.565 208.591 160.87 1 20 ? O5' ANP 601 A 1 
HETATM 14 C C5' ANP . . . L 5 169.514 209.997 160.821 1 20 ? C5' ANP 601 A 1 
HETATM 15 C C4' ANP . . . L 5 170.881 210.626 160.639 1 20 ? C4' ANP 601 A 1 
HETATM 16 O O4' ANP . . . L 5 171.13 210.915 159.26 1 20 ? O4' ANP 601 A 1 
HETATM 17 C C3' ANP . . . L 5 171.106 211.971 161.337 1 20 ? C3' ANP 601 A 1 
HETATM 18 O O3' ANP . . . L 5 172.422 212.228 161.684 1 20 ? O3' ANP 601 A 1 
HETATM 19 C C2' ANP . . . L 5 170.505 212.919 160.316 1 20 ? C2' ANP 601 A 1 
HETATM 20 O O2' ANP . . . L 5 170.998 214.21 160.526 1 20 ? O2' ANP 601 A 1 
HETATM 21 C C1' ANP . . . L 5 171.108 212.292 159.046 1 20 ? C1' ANP 601 A 1 
HETATM 22 N N9 ANP . . . L 5 170.319 212.581 157.854 1 20 ? N9 ANP 601 A 1 
HETATM 23 C C8 ANP . . . L 5 169.305 211.845 157.305 1 20 ? C8 ANP 601 A 1 
HETATM 24 N N7 ANP . . . L 5 168.802 212.378 156.23 1 20 ? N7 ANP 601 A 1 
HETATM 25 C C5 ANP . . . L 5 169.521 213.529 156.056 1 20 ? C5 ANP 601 A 1 
HETATM 26 C C6 ANP . . . L 5 169.479 214.548 155.093 1 20 ? C6 ANP 601 A 1 
HETATM 27 N N6 ANP . . . L 5 168.614 214.541 154.071 1 20 ? N6 ANP 601 A 1 
HETATM 28 N N1 ANP . . . L 5 170.339 215.562 155.21 1 20 ? N1 ANP 601 A 1 
HETATM 29 C C2 ANP . . . L 5 171.197 215.568 156.225 1 20 ? C2 ANP 601 A 1 
HETATM 30 N N3 ANP . . . L 5 171.334 214.674 157.187 1 20 ? N3 ANP 601 A 1 
HETATM 31 C C4 ANP . . . L 5 170.469 213.672 157.055 1 20 ? C4 ANP 601 A 1 
HETATM 32 H HNB1 ANP . . . L 5 170.995 204.045 159.219 1 20 ? HNB1 ANP 601 A 1 
HETATM 33 H "H5'1" ANP . . . L 5 169.121 210.376 161.623 1 20 ? "H5'1" ANP 601 A 1 
HETATM 34 H "H5'2" ANP . . . L 5 168.942 210.257 160.083 1 20 ? "H5'2" ANP 601 A 1 
HETATM 35 H H4' ANP . . . L 5 171.534 209.982 160.954 1 20 ? H4' ANP 601 A 1 
HETATM 36 H H3' ANP . . . L 5 170.526 212.021 162.113 1 20 ? H3' ANP 601 A 1 
HETATM 37 H HO3' ANP . . . L 5 172.629 212.889 161.191 1 20 ? HO3' ANP 601 A 1 
HETATM 38 H H2' ANP . . . L 5 169.536 212.892 160.3 1 20 ? H2' ANP 601 A 1 
HETATM 39 H HO2' ANP . . . L 5 171.091 214.593 159.773 1 20 ? HO2' ANP 601 A 1 
HETATM 40 H H1' ANP . . . L 5 172.003 212.625 158.875 1 20 ? H1' ANP 601 A 1 
HETATM 41 H H8 ANP . . . L 5 169.021 211.044 157.684 1 20 ? H8 ANP 601 A 1 
HETATM 42 H HN61 ANP . . . L 5 168.648 215.176 153.449 1 20 ? HN61 ANP 601 A 1 
HETATM 43 H HN62 ANP . . . L 5 167.995 213.907 153.995 1 20 ? HN62 ANP 601 A 1 
HETATM 44 H H2 ANP . . . L 5 171.773 216.297 156.257 1 20 ? H2 ANP 601 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           44 
#