data_5CB2
#
_model_server_result.job_id            MK-4zc2aTepsMrDEQJ2WSg 
_model_server_result.datetime_utc      '2025-02-27 12:56:51' 
_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          5cb2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":702}' 
#
_entry.id    5CB2 
#
_exptl.entry_id    5CB2 
_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    1 
_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            5CB2 
_cell.length_a            76.566 
_cell.length_b            120.926 
_cell.length_c            190.455 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5CB2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        24 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 6_555 -x,-y+1/2,z -1 0 0 0 -1 0 0 0 1 0 60.463 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 OG SER 72 A SER 72 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? 
metalc ? metalc2 A OG1 THR 95 A THR 95 1_555 B MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc3 B MG MG . A MG 701 1_555 C O1B GNP . A GNP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? 
metalc ? metalc4 B MG MG . A MG 701 1_555 C O1G GNP . A GNP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
#
_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                     5CB2 
_atom_sites.fract_transf_matrix[1][1]    0.013061 
_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]    0.00827 
_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]    0.005251 
_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 MG A 1 701 2 MG MG . 
C 3 GNP A 1 702 1001 GNP GNP . 
D 4 HOH A 1 801 17 HOH HOH . 
D 4 HOH A 2 802 18 HOH HOH . 
D 4 HOH A 3 803 7 HOH HOH . 
D 4 HOH A 4 804 16 HOH HOH . 
D 4 HOH A 5 805 4 HOH HOH . 
D 4 HOH A 6 806 11 HOH HOH . 
D 4 HOH A 7 807 15 HOH HOH . 
D 4 HOH A 8 808 3 HOH HOH . 
D 4 HOH A 9 809 2 HOH HOH . 
D 4 HOH A 10 810 19 HOH HOH . 
D 4 HOH A 11 811 13 HOH HOH . 
D 4 HOH A 12 812 5 HOH HOH . 
D 4 HOH A 13 813 8 HOH HOH . 
D 4 HOH A 14 814 21 HOH HOH . 
D 4 HOH A 15 815 20 HOH HOH . 
D 4 HOH A 16 816 14 HOH HOH . 
D 4 HOH A 17 817 1 HOH HOH . 
D 4 HOH A 18 818 6 HOH HOH . 
D 4 HOH A 19 819 12 HOH HOH . 
D 4 HOH A 20 820 10 HOH HOH . 
D 4 HOH A 21 821 22 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 . . . C 3 -10.672 21.449 -29.507 0.21 18 ? PG GNP 702 A 1 
HETATM 2 O O1G GNP . . . C 3 -11.183 20.16 -29.756 0.4 16.9 ? O1G GNP 702 A 1 
HETATM 3 O O2G GNP . . . C 3 -9.855 21.571 -28.257 0.65 19.06 ? O2G GNP 702 A 1 
HETATM 4 O O3G GNP . . . C 3 -11.929 22.332 -29.437 0.46 19.21 ? O3G GNP 702 A 1 
HETATM 5 N N3B GNP . . . C 3 -9.48 21.901 -30.56 0.75 24.32 ? N3B GNP 702 A 1 
HETATM 6 P PB GNP . . . C 3 -9.065 20.986 -31.923 0.51 22.3 ? PB GNP 702 A 1 
HETATM 7 O O1B GNP . . . C 3 -10.1 19.778 -31.9 0.49 24.24 ? O1B GNP 702 A 1 
HETATM 8 O O2B GNP . . . C 3 -7.603 20.864 -31.666 0.38 16.72 ? O2B GNP 702 A 1 
HETATM 9 O O3A GNP . . . C 3 -9.357 21.761 -33.265 0.8 26.18 ? O3A GNP 702 A 1 
HETATM 10 P PA GNP . . . C 3 -10.249 21.194 -34.498 0.6 29.93 ? PA GNP 702 A 1 
HETATM 11 O O1A GNP . . . C 3 -9.407 20.544 -35.504 0.74 21.01 ? O1A GNP 702 A 1 
HETATM 12 O O2A GNP . . . C 3 -11.587 20.71 -34.047 0.71 33.19 ? O2A GNP 702 A 1 
HETATM 13 O O5' GNP . . . C 3 -10.585 22.519 -35.277 1 40.95 ? O5' GNP 702 A 1 
HETATM 14 C C5' GNP . . . C 3 -9.532 23.524 -35.455 1 42.39 ? C5' GNP 702 A 1 
HETATM 15 C C4' GNP . . . C 3 -9.81 24.493 -36.604 1 33.31 ? C4' GNP 702 A 1 
HETATM 16 O O4' GNP . . . C 3 -8.577 24.767 -37.254 1 31.71 ? O4' GNP 702 A 1 
HETATM 17 C C3' GNP . . . C 3 -10.6 23.823 -37.672 1 34.68 ? C3' GNP 702 A 1 
HETATM 18 O O3' GNP . . . C 3 -11.573 24.759 -38.093 1 28.96 ? O3' GNP 702 A 1 
HETATM 19 C C2' GNP . . . C 3 -9.636 23.395 -38.755 1 31.28 ? C2' GNP 702 A 1 
HETATM 20 O O2' GNP . . . C 3 -10.283 23.664 -40 1 47.66 ? O2' GNP 702 A 1 
HETATM 21 C C1' GNP . . . C 3 -8.491 24.311 -38.595 1 29.46 ? C1' GNP 702 A 1 
HETATM 22 N N9 GNP . . . C 3 -7.214 23.685 -38.742 1 26.22 ? N9 GNP 702 A 1 
HETATM 23 C C8 GNP . . . C 3 -6.962 22.421 -38.555 1 27.62 ? C8 GNP 702 A 1 
HETATM 24 N N7 GNP . . . C 3 -5.654 22.182 -38.754 1 28.17 ? N7 GNP 702 A 1 
HETATM 25 C C5 GNP . . . C 3 -5.074 23.305 -39.041 1 24.53 ? C5 GNP 702 A 1 
HETATM 26 C C6 GNP . . . C 3 -3.722 23.668 -39.337 1 27.97 ? C6 GNP 702 A 1 
HETATM 27 O O6 GNP . . . C 3 -2.804 22.827 -39.361 1 29.59 ? O6 GNP 702 A 1 
HETATM 28 N N1 GNP . . . C 3 -3.509 24.937 -39.599 1 33.51 ? N1 GNP 702 A 1 
HETATM 29 C C2 GNP . . . C 3 -4.513 25.849 -39.593 1 37.53 ? C2 GNP 702 A 1 
HETATM 30 N N2 GNP . . . C 3 -4.217 27.149 -39.905 1 38.36 ? N2 GNP 702 A 1 
HETATM 31 N N3 GNP . . . C 3 -5.807 25.55 -39.329 1 30.34 ? N3 GNP 702 A 1 
HETATM 32 C C4 GNP . . . C 3 -6.106 24.306 -39.026 1 25.51 ? C4 GNP 702 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           32 
#