data_3DDC
#
_model_server_result.job_id            uPQDnUEdAsikoOgjFar4LQ 
_model_server_result.datetime_utc      '2025-01-02 19:19:51' 
_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          3ddc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":500}' 
#
_entry.id    3DDC 
#
_exptl.entry_id    3DDC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          4 
_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          125 
_cell.angle_gamma         90 
_cell.entry_id            3DDC 
_cell.length_a            79.6 
_cell.length_b            88 
_cell.length_c            56.5 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DDC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 tetrameric 4 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,B,C,D,E,F 1 1,2 
A,B,C,D,E,F 2 1 
#
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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 47.192931 0 46.282091 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 17 A SER 17 1_555 C MG MG . A MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc2 A OG1 THR 35 A THR 35 1_555 C MG MG . A MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc3 D O2G GNP . A GNP 500 1_555 C MG MG . A MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc4 D O2B GNP . A GNP 500 1_555 C MG MG . A MG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc5 C MG MG . A MG 600 1_555 E O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc6 C MG MG . A MG 600 1_555 E O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
#
_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                     3DDC 
_atom_sites.fract_transf_matrix[1][1]    0.012563 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.008797 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011364 
_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]    0.021607 
_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
C 3 MG A 1 600 600 MG MG . 
D 4 GNP A 1 500 500 GNP GNP . 
E 5 HOH A 1 601 1 HOH HOH . 
E 5 HOH A 2 602 2 HOH HOH . 
E 5 HOH A 3 603 3 HOH HOH . 
E 5 HOH A 4 604 4 HOH HOH . 
E 5 HOH A 5 605 5 HOH HOH . 
E 5 HOH A 6 606 8 HOH HOH . 
E 5 HOH A 7 607 9 HOH HOH . 
E 5 HOH A 8 608 10 HOH HOH . 
E 5 HOH A 9 609 11 HOH HOH . 
E 5 HOH A 10 610 12 HOH HOH . 
E 5 HOH A 11 611 13 HOH HOH . 
E 5 HOH A 12 612 14 HOH HOH . 
E 5 HOH A 13 613 20 HOH HOH . 
E 5 HOH A 14 614 21 HOH HOH . 
E 5 HOH A 15 615 22 HOH HOH . 
E 5 HOH A 16 616 26 HOH HOH . 
E 5 HOH A 17 617 27 HOH HOH . 
E 5 HOH A 18 618 28 HOH HOH . 
E 5 HOH A 19 619 29 HOH HOH . 
E 5 HOH A 20 620 31 HOH HOH . 
E 5 HOH A 21 621 32 HOH HOH . 
E 5 HOH A 22 622 33 HOH HOH . 
E 5 HOH A 23 623 37 HOH HOH . 
E 5 HOH A 24 624 38 HOH HOH . 
E 5 HOH A 25 625 39 HOH HOH . 
E 5 HOH A 26 626 45 HOH HOH . 
E 5 HOH A 27 627 47 HOH HOH . 
E 5 HOH A 28 628 48 HOH HOH . 
E 5 HOH A 29 629 49 HOH HOH . 
E 5 HOH A 30 630 50 HOH HOH . 
E 5 HOH A 31 631 51 HOH HOH . 
E 5 HOH A 32 632 52 HOH HOH . 
E 5 HOH A 33 633 53 HOH HOH . 
E 5 HOH A 34 634 54 HOH HOH . 
E 5 HOH A 35 635 57 HOH HOH . 
E 5 HOH A 36 636 58 HOH HOH . 
E 5 HOH A 37 637 59 HOH HOH . 
E 5 HOH A 38 638 60 HOH HOH . 
E 5 HOH A 39 639 61 HOH HOH . 
E 5 HOH A 40 640 62 HOH HOH . 
E 5 HOH A 41 641 64 HOH HOH . 
E 5 HOH A 42 642 65 HOH HOH . 
E 5 HOH A 43 643 66 HOH HOH . 
E 5 HOH A 44 644 69 HOH HOH . 
E 5 HOH A 45 645 70 HOH HOH . 
E 5 HOH A 46 646 71 HOH HOH . 
E 5 HOH A 47 647 74 HOH HOH . 
E 5 HOH A 48 648 75 HOH HOH . 
E 5 HOH A 49 649 76 HOH HOH . 
E 5 HOH A 50 650 77 HOH HOH . 
E 5 HOH A 51 651 82 HOH HOH . 
E 5 HOH A 52 652 84 HOH HOH . 
E 5 HOH A 53 653 89 HOH HOH . 
E 5 HOH A 54 654 90 HOH HOH . 
E 5 HOH A 55 655 92 HOH HOH . 
E 5 HOH A 56 656 93 HOH HOH . 
E 5 HOH A 57 657 95 HOH HOH . 
E 5 HOH A 58 658 96 HOH HOH . 
E 5 HOH A 59 659 97 HOH HOH . 
E 5 HOH A 60 660 98 HOH HOH . 
E 5 HOH A 61 661 102 HOH HOH . 
E 5 HOH A 62 662 107 HOH HOH . 
E 5 HOH A 63 663 108 HOH HOH . 
E 5 HOH A 64 664 114 HOH HOH . 
E 5 HOH A 65 665 115 HOH HOH . 
F 5 HOH B 1 6 6 HOH HOH . 
F 5 HOH B 2 7 7 HOH HOH . 
F 5 HOH B 3 15 15 HOH HOH . 
F 5 HOH B 4 16 16 HOH HOH . 
F 5 HOH B 5 17 17 HOH HOH . 
F 5 HOH B 6 18 18 HOH HOH . 
F 5 HOH B 7 19 19 HOH HOH . 
F 5 HOH B 8 23 23 HOH HOH . 
F 5 HOH B 9 24 24 HOH HOH . 
F 5 HOH B 10 25 25 HOH HOH . 
F 5 HOH B 11 30 30 HOH HOH . 
F 5 HOH B 12 34 34 HOH HOH . 
F 5 HOH B 13 35 35 HOH HOH . 
F 5 HOH B 14 36 36 HOH HOH . 
F 5 HOH B 15 40 40 HOH HOH . 
F 5 HOH B 16 41 41 HOH HOH . 
F 5 HOH B 17 42 42 HOH HOH . 
F 5 HOH B 18 43 43 HOH HOH . 
F 5 HOH B 19 44 44 HOH HOH . 
F 5 HOH B 20 46 46 HOH HOH . 
F 5 HOH B 21 55 55 HOH HOH . 
F 5 HOH B 22 56 56 HOH HOH . 
F 5 HOH B 23 63 63 HOH HOH . 
F 5 HOH B 24 67 67 HOH HOH . 
F 5 HOH B 25 68 68 HOH HOH . 
F 5 HOH B 26 72 72 HOH HOH . 
F 5 HOH B 27 73 73 HOH HOH . 
F 5 HOH B 28 78 78 HOH HOH . 
F 5 HOH B 29 79 79 HOH HOH . 
F 5 HOH B 30 80 80 HOH HOH . 
F 5 HOH B 31 81 81 HOH HOH . 
F 5 HOH B 32 83 83 HOH HOH . 
F 5 HOH B 33 85 85 HOH HOH . 
F 5 HOH B 34 86 86 HOH HOH . 
F 5 HOH B 35 87 87 HOH HOH . 
F 5 HOH B 36 88 88 HOH HOH . 
F 5 HOH B 37 91 91 HOH HOH . 
F 5 HOH B 38 94 94 HOH HOH . 
F 5 HOH B 39 99 99 HOH HOH . 
F 5 HOH B 40 100 100 HOH HOH . 
F 5 HOH B 41 101 101 HOH HOH . 
F 5 HOH B 42 103 103 HOH HOH . 
F 5 HOH B 43 104 104 HOH HOH . 
F 5 HOH B 44 105 105 HOH HOH . 
F 5 HOH B 45 106 106 HOH HOH . 
F 5 HOH B 46 109 109 HOH HOH . 
F 5 HOH B 47 110 110 HOH HOH . 
F 5 HOH B 48 111 111 HOH HOH . 
F 5 HOH B 49 112 112 HOH HOH . 
F 5 HOH B 50 113 113 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 . . . D 4 15.94 38.012 -2.746 1 14.68 ? PG GNP 500 A 1 
HETATM 2 O O1G GNP . . . D 4 14.632 37.577 -3.355 1 13.2 ? O1G GNP 500 A 1 
HETATM 3 O O2G GNP . . . D 4 16.097 37.579 -1.321 1 14.05 ? O2G GNP 500 A 1 
HETATM 4 O O3G GNP . . . D 4 16.137 39.464 -2.902 1 14.33 ? O3G GNP 500 A 1 
HETATM 5 N N3B GNP . . . D 4 17.164 37.337 -3.597 1 14.36 ? N3B GNP 500 A 1 
HETATM 6 P PB GNP . . . D 4 18.739 37.443 -3.28 1 15.11 ? PB GNP 500 A 1 
HETATM 7 O O1B GNP . . . D 4 19.369 38.73 -3.71 1 15.26 ? O1B GNP 500 A 1 
HETATM 8 O O2B GNP . . . D 4 19.018 37.105 -1.848 1 14.4 ? O2B GNP 500 A 1 
HETATM 9 O O3A GNP . . . D 4 19.421 36.329 -4.159 1 15.94 ? O3A GNP 500 A 1 
HETATM 10 P PA GNP . . . D 4 19.85 34.831 -3.797 1 16.61 ? PA GNP 500 A 1 
HETATM 11 O O1A GNP . . . D 4 21.037 34.912 -2.937 1 15.48 ? O1A GNP 500 A 1 
HETATM 12 O O2A GNP . . . D 4 18.672 34.074 -3.364 1 17.76 ? O2A GNP 500 A 1 
HETATM 13 O O5' GNP . . . D 4 20.38 34.259 -5.186 1 18.8 ? O5' GNP 500 A 1 
HETATM 14 C C5' GNP . . . D 4 19.512 34.067 -6.304 1 18.11 ? C5' GNP 500 A 1 
HETATM 15 C C4' GNP . . . D 4 20.119 33.017 -7.22 1 18.52 ? C4' GNP 500 A 1 
HETATM 16 O O4' GNP . . . D 4 21.393 33.516 -7.721 1 19.31 ? O4' GNP 500 A 1 
HETATM 17 C C3' GNP . . . D 4 20.398 31.671 -6.543 1 19.66 ? C3' GNP 500 A 1 
HETATM 18 O O3' GNP . . . D 4 19.9 30.643 -7.405 1 18.75 ? O3' GNP 500 A 1 
HETATM 19 C C2' GNP . . . D 4 21.904 31.722 -6.253 1 21.46 ? C2' GNP 500 A 1 
HETATM 20 O O2' GNP . . . D 4 22.57 30.475 -6.176 1 22.8 ? O2' GNP 500 A 1 
HETATM 21 C C1' GNP . . . D 4 22.42 32.568 -7.415 1 19.12 ? C1' GNP 500 A 1 
HETATM 22 N N9 GNP . . . D 4 23.614 33.307 -7.071 1 19.45 ? N9 GNP 500 A 1 
HETATM 23 C C8 GNP . . . D 4 23.826 34.179 -6.014 1 17.78 ? C8 GNP 500 A 1 
HETATM 24 N N7 GNP . . . D 4 25.03 34.673 -5.978 1 18.67 ? N7 GNP 500 A 1 
HETATM 25 C C5 GNP . . . D 4 25.667 34.087 -7.057 1 19.3 ? C5 GNP 500 A 1 
HETATM 26 C C6 GNP . . . D 4 26.994 34.258 -7.559 1 20.32 ? C6 GNP 500 A 1 
HETATM 27 O O6 GNP . . . D 4 27.904 34.938 -7.088 1 20.49 ? O6 GNP 500 A 1 
HETATM 28 N N1 GNP . . . D 4 27.224 33.475 -8.687 1 20.59 ? N1 GNP 500 A 1 
HETATM 29 C C2 GNP . . . D 4 26.291 32.651 -9.274 1 19.77 ? C2 GNP 500 A 1 
HETATM 30 N N2 GNP . . . D 4 26.673 31.96 -10.382 1 20.63 ? N2 GNP 500 A 1 
HETATM 31 N N3 GNP . . . D 4 25.034 32.502 -8.842 1 19.67 ? N3 GNP 500 A 1 
HETATM 32 C C4 GNP . . . D 4 24.81 33.243 -7.729 1 18.47 ? C4 GNP 500 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           32 
#