data_7KDC
#
_model_server_result.job_id            1gN2GLLAGkxns-HxmIL4NQ 
_model_server_result.datetime_utc      '2025-03-29 06:24:05' 
_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          7kdc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":201}' 
#
_entry.id    7KDC 
#
_exptl.entry_id    7KDC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE 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         120 
_cell.entry_id            7KDC 
_cell.length_a            82.81 
_cell.length_b            82.81 
_cell.length_c            136.761 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KDC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        144 
_symmetry.space_group_name_Hall    'P 31' 
_symmetry.space_group_name_H-M     'P 31' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,F,G,K,M 1 1 
B,D,H,I,J,L,N 2 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 E N N 
? 3 H 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 C SG CYS 46 C CYS 1508 1_555 D SG CYS 48 D CYS 1510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 C SG CYS 48 C CYS 1510 1_555 D SG CYS 46 D CYS 1508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc1 A OG1 THR 28 A THR 31 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc2 A OG1 THR 46 A THR 49 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc3 E O2G GNP . A GNP 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc4 E O2B GNP . A GNP 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc5 F MG MG . A MG 202 1_555 K O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc6 B OG1 THR 28 B THR 31 1_555 I MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc7 B OG1 THR 46 B THR 49 1_555 I MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc8 H O2G GNP . B GNP 201 1_555 I MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc9 H O2B GNP . B GNP 201 1_555 I MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc10 I MG MG . B MG 202 1_555 L O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
#
_chem_comp.formula           'C10 H17 N6 O13 P3' 
_chem_comp.formula_weight    522.196 
_chem_comp.id                GNP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE 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 GNP doub 129 n n 
PG O2G GNP sing 130 n n 
PG O3G GNP sing 131 n n 
PG N3B GNP sing 132 n n 
O2G HOG2 GNP sing 133 n n 
O3G HOG3 GNP sing 134 n n 
N3B PB GNP sing 135 n n 
N3B HNB3 GNP sing 136 n n 
PB O1B GNP doub 137 n n 
PB O2B GNP sing 138 n n 
PB O3A GNP sing 139 n n 
O2B HOB2 GNP sing 140 n n 
O3A PA GNP sing 141 n n 
PA O1A GNP doub 142 n n 
PA O2A GNP sing 143 n n 
PA O5' GNP sing 144 n n 
O2A HOA2 GNP sing 145 n n 
O5' C5' GNP sing 146 n n 
C5' C4' GNP sing 147 n n 
C5' "H5'2" GNP sing 148 n n 
C5' "H5'1" GNP sing 149 n n 
C4' O4' GNP sing 150 n n 
C4' C3' GNP sing 151 n n 
C4' H4' GNP sing 152 n n 
O4' C1' GNP sing 153 n n 
C3' O3' GNP sing 154 n n 
C3' C2' GNP sing 155 n n 
C3' H3' GNP sing 156 n n 
O3' HO3' GNP sing 157 n n 
C2' O2' GNP sing 158 n n 
C2' C1' GNP sing 159 n n 
C2' H2' GNP sing 160 n n 
O2' HO2' GNP sing 161 n n 
C1' N9 GNP sing 162 n n 
C1' H1' GNP sing 163 n n 
N9 C8 GNP sing 164 n y 
N9 C4 GNP sing 165 n y 
C8 N7 GNP doub 166 n y 
C8 H8 GNP sing 167 n n 
N7 C5 GNP sing 168 n y 
C5 C6 GNP sing 169 n y 
C5 C4 GNP doub 170 n y 
C6 O6 GNP doub 171 n n 
C6 N1 GNP sing 172 n y 
N1 C2 GNP sing 173 n y 
N1 HN1 GNP sing 174 n n 
C2 N2 GNP sing 175 n n 
C2 N3 GNP doub 176 n y 
N2 HN21 GNP sing 177 n n 
N2 HN22 GNP sing 178 n n 
N3 C4 GNP sing 179 n y 
#
_atom_sites.entry_id                     7KDC 
_atom_sites.fract_transf_matrix[1][1]    0.012076 
_atom_sites.fract_transf_matrix[1][2]    0.006972 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013944 
_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]    0.007312 
_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
E 3 GNP A 1 201 201 GNP GNP . 
F 4 MG A 1 202 202 MG MG . 
G 4 MG A 1 203 1 MG MG . 
H 3 GNP B 1 201 201 GNP GNP . 
I 4 MG B 1 202 202 MG MG . 
J 4 MG B 1 203 2 MG MG . 
K 5 HOH A 1 301 11 HOH HOH . 
K 5 HOH A 2 302 10 HOH HOH . 
K 5 HOH A 3 303 1 HOH HOH . 
L 5 HOH B 1 301 12 HOH HOH . 
L 5 HOH B 2 302 8 HOH HOH . 
L 5 HOH B 3 303 2 HOH HOH . 
M 5 HOH C 1 1901 14 HOH HOH . 
N 5 HOH D 1 1901 15 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 P PG GNP . . . H 3 -27.356 58.46 -74.404 1 108.24 ? PG GNP 201 B 1 
HETATM 2 O O1G GNP . . . H 3 -28.649 59.212 -74.282 1 100.91 ? O1G GNP 201 B 1 
HETATM 3 O O2G GNP . . . H 3 -26.188 59.4 -74.106 1 101.23 ? O2G GNP 201 B 1 
HETATM 4 O O3G GNP . . . H 3 -27.354 57.282 -73.393 1 115.59 ? O3G GNP 201 B 1 
HETATM 5 N N3B GNP . . . H 3 -27.196 57.843 -75.99 1 119.02 ? N3B GNP 201 B 1 
HETATM 6 P PB GNP . . . H 3 -27.226 58.868 -77.269 1 111.21 ? PB GNP 201 B 1 
HETATM 7 O O1B GNP . . . H 3 -28.598 59.476 -77.401 1 102.47 ? O1B GNP 201 B 1 
HETATM 8 O O2B GNP . . . H 3 -26.202 59.951 -77.057 1 110.75 ? O2B GNP 201 B 1 
HETATM 9 O O3A GNP . . . H 3 -26.876 58.041 -78.646 1 116.44 ? O3A GNP 201 B 1 
HETATM 10 P PA GNP . . . H 3 -25.462 58.126 -79.366 1 113.22 ? PA GNP 201 B 1 
HETATM 11 O O1A GNP . . . H 3 -25.392 59.487 -80.054 1 119.27 ? O1A GNP 201 B 1 
HETATM 12 O O2A GNP . . . H 3 -24.361 57.827 -78.425 1 118.74 ? O2A GNP 201 B 1 
HETATM 13 O O5' GNP . . . H 3 -25.555 57.013 -80.476 1 116.69 ? O5' GNP 201 B 1 
HETATM 14 C C5' GNP . . . H 3 -26.154 55.729 -80.203 1 104.25 ? C5' GNP 201 B 1 
HETATM 15 C C4' GNP . . . H 3 -25.804 54.758 -81.305 1 123.27 ? C4' GNP 201 B 1 
HETATM 16 O O4' GNP . . . H 3 -26.537 55.094 -82.506 1 127.37 ? O4' GNP 201 B 1 
HETATM 17 C C3' GNP . . . H 3 -24.33 54.7 -81.704 1 131.27 ? C3' GNP 201 B 1 
HETATM 18 O O3' GNP . . . H 3 -23.925 53.366 -81.991 1 134.25 ? O3' GNP 201 B 1 
HETATM 19 C C2' GNP . . . H 3 -24.273 55.595 -82.946 1 124.43 ? C2' GNP 201 B 1 
HETATM 20 O O2' GNP . . . H 3 -23.231 55.203 -83.834 1 125.51 ? O2' GNP 201 B 1 
HETATM 21 C C1' GNP . . . H 3 -25.642 55.335 -83.575 1 114.42 ? C1' GNP 201 B 1 
HETATM 22 N N9 GNP . . . H 3 -26.151 56.477 -84.353 1 116.69 ? N9 GNP 201 B 1 
HETATM 23 C C8 GNP . . . H 3 -26.374 57.751 -83.899 1 111.82 ? C8 GNP 201 B 1 
HETATM 24 N N7 GNP . . . H 3 -26.831 58.559 -84.828 1 116.42 ? N7 GNP 201 B 1 
HETATM 25 C C5 GNP . . . H 3 -26.914 57.767 -85.96 1 123.67 ? C5 GNP 201 B 1 
HETATM 26 C C6 GNP . . . H 3 -27.346 58.072 -87.304 1 105.64 ? C6 GNP 201 B 1 
HETATM 27 O O6 GNP . . . H 3 -27.747 59.153 -87.734 1 104.58 ? O6 GNP 201 B 1 
HETATM 28 N N1 GNP . . . H 3 -27.269 56.971 -88.132 1 101.47 ? N1 GNP 201 B 1 
HETATM 29 C C2 GNP . . . H 3 -26.837 55.727 -87.755 1 110.62 ? C2 GNP 201 B 1 
HETATM 30 N N2 GNP . . . H 3 -26.829 54.78 -88.694 1 125.63 ? N2 GNP 201 B 1 
HETATM 31 N N3 GNP . . . H 3 -26.436 55.43 -86.519 1 118.69 ? N3 GNP 201 B 1 
HETATM 32 C C4 GNP . . . H 3 -26.499 56.482 -85.682 1 129.25 ? C4 GNP 201 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           32 
#