data_5OF3
#
_model_server_result.job_id            PqcXqL7xfcKDz716uyNQoA 
_model_server_result.datetime_utc      '2025-02-05 09:59:37' 
_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          5of3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1001}' 
#
_entry.id    5OF3 
#
_exptl.entry_id    5OF3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              505.208 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' 
_entity.pdbx_number_of_molecules    4 
_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            5OF3 
_cell.length_a            104.889 
_cell.length_b            104.889 
_cell.length_c            229.758 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5OF3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               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 
_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
? 4 G N N 
? 4 J N N 
? 4 M N N 
? 4 O 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
disulf ? disulf1 B SG CYS 120 B CYS 120 1_555 B SG CYS 139 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 C SG CYS 108 D CYS 108 1_555 C SG CYS 145 D CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf3 C SG CYS 184 D CYS 184 1_555 C SG CYS 188 D CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf4 D SG CYS 120 E CYS 120 1_555 D SG CYS 139 E CYS 139 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc1 A OD1 ASP 101 A ASP 101 1_555 H MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc2 A OD1 ASP 103 A ASP 103 1_555 H MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc3 A SG CYS 116 A CYS 116 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc4 A SG CYS 119 A CYS 119 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc5 A SG CYS 128 A CYS 128 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc6 A OD2 ASP 131 A ASP 131 1_555 I ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc7 G O1G APC . A APC 1001 1_555 H MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? 
metalc ? metalc8 G O1B APC . A APC 1001 1_555 H MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc9 G O1A APC . A APC 1001 1_555 H MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
metalc ? metalc10 C OD1 ASP 101 D ASP 101 1_555 K MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc11 C OD1 ASP 103 D ASP 103 1_555 K MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc12 C SG CYS 116 D CYS 116 1_555 L ZN ZN . D ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc13 C SG CYS 119 D CYS 119 1_555 L ZN ZN . D ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc14 C SG CYS 128 D CYS 128 1_555 L ZN ZN . D ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc15 C OD2 ASP 131 D ASP 131 1_555 L ZN ZN . D ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc16 J O2G APC . D APC 1001 1_555 K MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc17 J O2B APC . D APC 1001 1_555 K MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc18 J O2A APC . D APC 1001 1_555 K MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc19 E O ASP 70 C ASP 70 1_555 N MN MN . C MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc20 E OD1 ASP 70 C ASP 70 1_555 N MN MN . C MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc21 M O2G APC . C APC 1001 1_555 N MN MN . C MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc22 M O2B APC . C APC 1001 1_555 N MN MN . C MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc23 M O2A APC . C APC 1001 1_555 N MN MN . C MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc24 F O ASP 70 F ASP 70 1_555 P MN MN . F MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
metalc ? metalc25 F OD1 ASP 70 F ASP 70 1_555 P MN MN . F MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc26 O O1G APC . F APC 1001 1_555 P MN MN . F MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc27 O O1B APC . F APC 1001 1_555 P MN MN . F MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? 
metalc ? metalc28 O O1A APC . F APC 1001 1_555 P MN MN . F MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
#
_chem_comp.formula           'C11 H18 N5 O12 P3' 
_chem_comp.formula_weight    505.208 
_chem_comp.id                APC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" 
#
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 APC doub 13 n n 
PG O2G APC sing 14 n n 
PG O3G APC sing 15 n n 
PG O3B APC sing 16 n n 
O2G HOG2 APC sing 17 n n 
O3G HOG3 APC sing 18 n n 
PB O1B APC doub 19 n n 
PB O2B APC sing 20 n n 
PB O3B APC sing 21 n n 
PB C3A APC sing 22 n n 
O2B HOB2 APC sing 23 n n 
PA O1A APC doub 24 n n 
PA O2A APC sing 25 n n 
PA C3A APC sing 26 n n 
PA O5' APC sing 27 n n 
O2A HOA2 APC sing 28 n n 
C3A H3A1 APC sing 29 n n 
C3A H3A2 APC sing 30 n n 
O5' C5' APC sing 31 n n 
C5' C4' APC sing 32 n n 
C5' "H5'1" APC sing 33 n n 
C5' "H5'2" APC sing 34 n n 
C4' O4' APC sing 35 n n 
C4' C3' APC sing 36 n n 
C4' H4' APC sing 37 n n 
O4' C1' APC sing 38 n n 
C3' O3' APC sing 39 n n 
C3' C2' APC sing 40 n n 
C3' H3' APC sing 41 n n 
O3' HO3' APC sing 42 n n 
C2' O2' APC sing 43 n n 
C2' C1' APC sing 44 n n 
C2' H2' APC sing 45 n n 
O2' HO2' APC sing 46 n n 
C1' N9 APC sing 47 n n 
C1' H1' APC sing 48 n n 
N9 C8 APC sing 49 n y 
N9 C4 APC sing 50 n y 
C8 N7 APC doub 51 n y 
C8 H8 APC sing 52 n n 
N7 C5 APC sing 53 n y 
C5 C6 APC sing 54 n y 
C5 C4 APC doub 55 n y 
C6 N6 APC sing 56 n n 
C6 N1 APC doub 57 n y 
N6 HN61 APC sing 58 n n 
N6 HN62 APC sing 59 n n 
N1 C2 APC sing 60 n y 
C2 N3 APC doub 61 n y 
C2 H2 APC sing 62 n n 
N3 C4 APC sing 63 n y 
#
_atom_sites.entry_id                     5OF3 
_atom_sites.fract_transf_matrix[1][1]    0.009534 
_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]    0.009534 
_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]    0.004352 
_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 4 APC A 1 1001 1001 APC APC . 
H 5 MN A 1 1002 1002 MN MN . 
I 6 ZN A 1 1003 1003 ZN ZN . 
J 4 APC D 1 1001 1001 APC APC . 
K 5 MN D 1 1002 1002 MN MN . 
L 6 ZN D 1 1003 1003 ZN ZN . 
M 4 APC C 1 1001 1001 APC APC . 
N 5 MN C 1 1002 1002 MN MN . 
O 4 APC F 1 1001 1001 APC APC . 
P 5 MN F 1 1002 1002 MN MN . 
#
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 APC . . . J 4 26.186 34.987 14.972 0.99 67.56 ? PG APC 1001 D 1 
HETATM 2 O O1G APC . . . J 4 26.385 35.725 13.689 0.99 75.42 ? O1G APC 1001 D 1 
HETATM 3 O O2G APC . . . J 4 25.336 33.721 14.805 0.99 69.4 ? O2G APC 1001 D 1 
HETATM 4 O O3G APC . . . J 4 25.537 35.847 16.058 0.99 78.72 ? O3G APC 1001 D 1 
HETATM 5 P PB APC . . . J 4 28.311 33.097 15.641 0.99 62.39 ? PB APC 1001 D 1 
HETATM 6 O O1B APC . . . J 4 29.697 33.209 16.241 0.99 56.39 ? O1B APC 1001 D 1 
HETATM 7 O O2B APC . . . J 4 27.444 32.215 16.585 0.99 53.85 ? O2B APC 1001 D 1 
HETATM 8 O O3B APC . . . J 4 27.586 34.516 15.568 0.99 42.96 ? O3B APC 1001 D 1 
HETATM 9 P PA APC . . . J 4 27.409 30.765 13.89 0.99 75.83 ? PA APC 1001 D 1 
HETATM 10 O O1A APC . . . J 4 27.705 30.262 12.449 0.99 72.27 ? O1A APC 1001 D 1 
HETATM 11 O O2A APC . . . J 4 25.929 30.567 14.152 0.99 86.36 ? O2A APC 1001 D 1 
HETATM 12 C C3A APC . . . J 4 28.092 32.425 13.988 0.99 69.17 ? C3A APC 1001 D 1 
HETATM 13 O O5' APC . . . J 4 28.339 29.929 14.844 0.99 66.25 ? O5' APC 1001 D 1 
HETATM 14 C C5' APC . . . J 4 27.849 28.801 15.599 0.99 59.23 ? C5' APC 1001 D 1 
HETATM 15 C C4' APC . . . J 4 29.013 28.117 16.271 0.99 61.07 ? C4' APC 1001 D 1 
HETATM 16 O O4' APC . . . J 4 30.129 28.044 15.355 0.99 73.42 ? O4' APC 1001 D 1 
HETATM 17 C C3' APC . . . J 4 29.547 28.791 17.533 0.99 65.38 ? C3' APC 1001 D 1 
HETATM 18 O O3' APC . . . J 4 30.015 27.822 18.465 0.99 68.8 ? O3' APC 1001 D 1 
HETATM 19 C C2' APC . . . J 4 30.693 29.649 16.995 0.99 70.72 ? C2' APC 1001 D 1 
HETATM 20 O O2' APC . . . J 4 31.698 29.864 17.979 0.99 74.43 ? O2' APC 1001 D 1 
HETATM 21 C C1' APC . . . J 4 31.234 28.762 15.873 0.99 75.02 ? C1' APC 1001 D 1 
HETATM 22 N N9 APC . . . J 4 31.852 29.502 14.779 0.99 68.33 ? N9 APC 1001 D 1 
HETATM 23 C C8 APC . . . J 4 31.622 30.806 14.43 0.99 68.82 ? C8 APC 1001 D 1 
HETATM 24 N N7 APC . . . J 4 32.319 31.216 13.397 0.99 78.03 ? N7 APC 1001 D 1 
HETATM 25 C C5 APC . . . J 4 33.06 30.1 13.04 0.99 69.18 ? C5 APC 1001 D 1 
HETATM 26 C C6 APC . . . J 4 34 29.872 12.015 0.99 66.66 ? C6 APC 1001 D 1 
HETATM 27 N N6 APC . . . J 4 34.364 30.797 11.122 0.99 72.72 ? N6 APC 1001 D 1 
HETATM 28 N N1 APC . . . J 4 34.556 28.644 11.935 0.99 77.08 ? N1 APC 1001 D 1 
HETATM 29 C C2 APC . . . J 4 34.192 27.714 12.822 0.99 59.03 ? C2 APC 1001 D 1 
HETATM 30 N N3 APC . . . J 4 33.319 27.811 13.828 0.99 66.28 ? N3 APC 1001 D 1 
HETATM 31 C C4 APC . . . J 4 32.785 29.036 13.882 0.99 69.15 ? C4 APC 1001 D 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           264 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#