data_6PFJ
#
_model_server_result.job_id            3tRfTxtODcZOqHtuOS0kFQ 
_model_server_result.datetime_utc      '2024-12-27 02:31:17' 
_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          6pfj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":202}' 
#
_entry.id    6PFJ 
#
_exptl.entry_id    6PFJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              690.411 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" 
_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            6PFJ 
_cell.length_a            92.089 
_cell.length_b            92.089 
_cell.length_c            96.646 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        172 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 64' 
#
_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,E,F 
_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
? 3 C N N 
? 3 D N N 
#
_chem_comp.formula           'C20 H24 N10 O14 P2' 
_chem_comp.formula_weight    690.411 
_chem_comp.id                C2E 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'c-di-GMP;Cyclic diguanosine monophosphate' 
#
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
P1 O2P C2E sing 70 n n 
O1P P1 C2E doub 71 n n 
O5' P1 C2E sing 72 n n 
C5' O5' C2E sing 73 n n 
C4' O4' C2E sing 74 n n 
C4' C5' C2E sing 75 n n 
C3' C4' C2E sing 76 n n 
O3' P11 C2E sing 77 n n 
O3' C3' C2E sing 78 n n 
C2' C3' C2E sing 79 n n 
C2' C1' C2E sing 80 n n 
O2' C2' C2E sing 81 n n 
C1' O4' C2E sing 82 n n 
C1' N9 C2E sing 83 n n 
N9 C4 C2E sing 84 n y 
N9 C8 C2E sing 85 n y 
C8 N7 C2E doub 86 n y 
C5 N7 C2E sing 87 n y 
C5 C6 C2E sing 88 n n 
C6 O6 C2E doub 89 n n 
N1 C6 C2E sing 90 n n 
C2 N1 C2E sing 91 n n 
N2 C2 C2E sing 92 n n 
N3 C2 C2E doub 93 n n 
N3 C4 C2E sing 94 n n 
C4 C5 C2E doub 95 n y 
P11 O21 C2E sing 96 n n 
P11 O5A C2E sing 97 n n 
O11 P11 C2E doub 98 n n 
C5A O5A C2E sing 99 n n 
C5A C4A C2E sing 100 n n 
C4A O4A C2E sing 101 n n 
C4A C3A C2E sing 102 n n 
O4A C1A C2E sing 103 n n 
C3A C2A C2E sing 104 n n 
O3A C3A C2E sing 105 n n 
O3A P1 C2E sing 106 n n 
C2A O2A C2E sing 107 n n 
C1A C2A C2E sing 108 n n 
C1A N91 C2E sing 109 n n 
N91 C41 C2E sing 110 n y 
C81 N71 C2E doub 111 n y 
C81 N91 C2E sing 112 n y 
N71 C51 C2E sing 113 n y 
C51 C41 C2E doub 114 n y 
C51 C61 C2E sing 115 n n 
C61 O61 C2E doub 116 n n 
C61 N11 C2E sing 117 n n 
C21 N11 C2E sing 118 n n 
C21 N21 C2E sing 119 n n 
N31 C21 C2E doub 120 n n 
C41 N31 C2E sing 121 n n 
O2P HO2P C2E sing 122 n n 
C5' "H5'1" C2E sing 123 n n 
C5' "H5'2" C2E sing 124 n n 
C4' H4' C2E sing 125 n n 
C3' H3' C2E sing 126 n n 
C2' H2' C2E sing 127 n n 
O2' HO2' C2E sing 128 n n 
C1' H1' C2E sing 129 n n 
C8 H8 C2E sing 130 n n 
N1 HN1 C2E sing 131 n n 
N2 HN21 C2E sing 132 n n 
N2 HN22 C2E sing 133 n n 
O21 HO21 C2E sing 134 n n 
C5A H511 C2E sing 135 n n 
C5A H512 C2E sing 136 n n 
C4A H4A C2E sing 137 n n 
C3A H3A C2E sing 138 n n 
C2A H2A C2E sing 139 n n 
O2A HO2A C2E sing 140 n n 
C1A H1A C2E sing 141 n n 
C81 H81 C2E sing 142 n n 
N11 HN11 C2E sing 143 n n 
N21 HN24 C2E sing 144 n n 
N21 HN23 C2E sing 145 n n 
#
_atom_sites.entry_id                     6PFJ 
_atom_sites.fract_transf_matrix[1][1]    0.010859 
_atom_sites.fract_transf_matrix[1][2]    0.006269 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012539 
_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]    0.010347 
_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 C2E T 1 201 201 C2E C2E . 
D 3 C2E T 1 202 202 C2E C2E . 
E 4 HOH T 1 301 301 HOH HOH . 
E 4 HOH T 2 302 302 HOH HOH . 
E 4 HOH T 3 303 303 HOH HOH . 
E 4 HOH T 4 304 304 HOH HOH . 
E 4 HOH T 5 305 305 HOH HOH . 
E 4 HOH T 6 306 306 HOH HOH . 
E 4 HOH T 7 307 307 HOH HOH . 
E 4 HOH T 8 308 308 HOH HOH . 
E 4 HOH T 9 309 309 HOH HOH . 
E 4 HOH T 10 310 310 HOH HOH . 
E 4 HOH T 11 311 311 HOH HOH . 
E 4 HOH T 12 312 312 HOH HOH . 
E 4 HOH T 13 313 313 HOH HOH . 
E 4 HOH T 14 314 314 HOH HOH . 
E 4 HOH T 15 315 315 HOH HOH . 
E 4 HOH T 16 316 316 HOH HOH . 
E 4 HOH T 17 317 317 HOH HOH . 
E 4 HOH T 18 318 318 HOH HOH . 
E 4 HOH T 19 319 319 HOH HOH . 
E 4 HOH T 20 320 320 HOH HOH . 
F 4 HOH A 1 301 301 HOH HOH . 
F 4 HOH A 2 302 302 HOH HOH . 
F 4 HOH A 3 303 303 HOH HOH . 
F 4 HOH A 4 304 304 HOH HOH . 
F 4 HOH A 5 305 305 HOH HOH . 
F 4 HOH A 6 306 306 HOH HOH . 
F 4 HOH A 7 307 307 HOH HOH . 
F 4 HOH A 8 308 308 HOH HOH . 
F 4 HOH A 9 309 309 HOH HOH . 
F 4 HOH A 10 310 310 HOH HOH . 
F 4 HOH A 11 311 311 HOH HOH . 
F 4 HOH A 12 312 312 HOH HOH . 
F 4 HOH A 13 313 313 HOH HOH . 
F 4 HOH A 14 314 314 HOH HOH . 
F 4 HOH A 15 315 315 HOH HOH . 
F 4 HOH A 16 316 316 HOH HOH . 
F 4 HOH A 17 317 317 HOH HOH . 
F 4 HOH A 18 318 318 HOH HOH . 
F 4 HOH A 19 319 319 HOH HOH . 
F 4 HOH A 20 320 320 HOH HOH . 
F 4 HOH A 21 321 321 HOH HOH . 
F 4 HOH A 22 322 322 HOH HOH . 
F 4 HOH A 23 323 323 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 P1 C2E . . . D 3 -19.535 -4.232 4.708 1 45.91 ? P1 C2E 202 T 1 
HETATM 2 O O2P C2E . . . D 3 -20.192 -5.578 4.662 1 43.69 ? O2P C2E 202 T 1 
HETATM 3 O O1P C2E . . . D 3 -18.21 -3.916 5.319 1 50.4 ? O1P C2E 202 T 1 
HETATM 4 O O5' C2E . . . D 3 -20.645 -3.443 5.496 1 45.83 ? O5' C2E 202 T 1 
HETATM 5 C C5' C2E . . . D 3 -21.061 -2.499 5.019 1 59.56 ? C5' C2E 202 T 1 
HETATM 6 C C4' C2E . . . D 3 -22.343 -1.923 5.612 1 46.99 ? C4' C2E 202 T 1 
HETATM 7 O O4' C2E . . . D 3 -22.574 -2.167 7.025 1 44.13 ? O4' C2E 202 T 1 
HETATM 8 C C3' C2E . . . D 3 -22.025 -0.432 5.48 1 42.4 ? C3' C2E 202 T 1 
HETATM 9 O O3' C2E . . . D 3 -22.575 0.015 4.385 1 41.52 ? O3' C2E 202 T 1 
HETATM 10 C C2' C2E . . . D 3 -22.438 0.295 6.756 1 37.59 ? C2' C2E 202 T 1 
HETATM 11 O O2' C2E . . . D 3 -23.605 0.968 6.535 1 39.25 ? O2' C2E 202 T 1 
HETATM 12 C C1' C2E . . . D 3 -22.567 -0.95 7.762 1 42.12 ? C1' C2E 202 T 1 
HETATM 13 N N9 C2E . . . D 3 -21.406 -1.173 8.668 1 40.34 ? N9 C2E 202 T 1 
HETATM 14 C C8 C2E . . . D 3 -20.026 -1.352 8.391 1 41.77 ? C8 C2E 202 T 1 
HETATM 15 N N7 C2E . . . D 3 -19.347 -1.588 9.479 1 37.58 ? N7 C2E 202 T 1 
HETATM 16 C C5 C2E . . . D 3 -20.241 -1.588 10.504 1 39.66 ? C5 C2E 202 T 1 
HETATM 17 C C6 C2E . . . D 3 -19.968 -1.811 11.855 1 49.13 ? C6 C2E 202 T 1 
HETATM 18 O O6 C2E . . . D 3 -18.902 -2.063 12.386 1 48.13 ? O6 C2E 202 T 1 
HETATM 19 N N1 C2E . . . D 3 -21.154 -1.769 12.664 1 46.48 ? N1 C2E 202 T 1 
HETATM 20 C C2 C2E . . . D 3 -22.387 -1.5 12.09 1 42.39 ? C2 C2E 202 T 1 
HETATM 21 N N2 C2E . . . D 3 -23.492 -1.455 12.909 1 44.39 ? N2 C2E 202 T 1 
HETATM 22 N N3 C2E . . . D 3 -22.633 -1.279 10.794 1 45.53 ? N3 C2E 202 T 1 
HETATM 23 C C4 C2E . . . D 3 -21.503 -1.339 10.053 1 43.29 ? C4 C2E 202 T 1 
HETATM 24 P P11 C2E . . . D 3 -21.727 1.014 3.394 1 44.37 ? P11 C2E 202 T 1 
HETATM 25 O O21 C2E . . . D 3 -22.63 1.375 2.26 1 38.77 ? O21 C2E 202 T 1 
HETATM 26 O O11 C2E . . . D 3 -20.992 2.017 4.224 1 41.4 ? O11 C2E 202 T 1 
HETATM 27 O O5A C2E . . . D 3 -20.566 -0.054 2.874 1 43.74 ? O5A C2E 202 T 1 
HETATM 28 C C5A C2E . . . D 3 -20.821 -0.904 1.755 1 45.47 ? C5A C2E 202 T 1 
HETATM 29 C C4A C2E . . . D 3 -19.587 -1.808 1.577 1 43.73 ? C4A C2E 202 T 1 
HETATM 30 O O4A C2E . . . D 3 -18.61 -0.931 1.073 1 44.39 ? O4A C2E 202 T 1 
HETATM 31 C C3A C2E . . . D 3 -18.978 -2.386 2.811 1 42.97 ? C3A C2E 202 T 1 
HETATM 32 O O3A C2E . . . D 3 -19.557 -3.602 3.191 1 41.79 ? O3A C2E 202 T 1 
HETATM 33 C C2A C2E . . . D 3 -17.487 -2.586 2.301 1 48.5 ? C2A C2E 202 T 1 
HETATM 34 O O2A C2E . . . D 3 -17.355 -3.723 1.465 1 50.11 ? O2A C2E 202 T 1 
HETATM 35 C C1A C2E . . . D 3 -17.328 -1.358 1.445 1 47.33 ? C1A C2E 202 T 1 
HETATM 36 N N91 C2E . . . D 3 -16.719 -0.272 2.256 1 45.62 ? N91 C2E 202 T 1 
HETATM 37 C C81 C2E . . . D 3 -17.359 0.733 2.953 1 42.07 ? C81 C2E 202 T 1 
HETATM 38 N N71 C2E . . . D 3 -16.47 1.561 3.569 1 43.69 ? N71 C2E 202 T 1 
HETATM 39 C C51 C2E . . . D 3 -15.231 1.058 3.235 1 44.79 ? C51 C2E 202 T 1 
HETATM 40 C C61 C2E . . . D 3 -13.968 1.551 3.622 1 45.15 ? C61 C2E 202 T 1 
HETATM 41 O O61 C2E . . . D 3 -13.665 2.507 4.293 1 53.24 ? O61 C2E 202 T 1 
HETATM 42 N N11 C2E . . . D 3 -12.937 0.833 3.11 1 49.73 ? N11 C2E 202 T 1 
HETATM 43 C C21 C2E . . . D 3 -13.124 -0.284 2.265 1 56.19 ? C21 C2E 202 T 1 
HETATM 44 N N21 C2E . . . D 3 -11.955 -0.924 1.786 1 50.85 ? N21 C2E 202 T 1 
HETATM 45 N N31 C2E . . . D 3 -14.333 -0.794 1.885 1 46.37 ? N31 C2E 202 T 1 
HETATM 46 C C41 C2E . . . D 3 -15.359 -0.071 2.416 1 43.71 ? C41 C2E 202 T 1 
HETATM 47 H "H5'1" C2E . . . D 3 -21.187 -2.651 4.07 1 71.45 ? "H5'1" C2E 202 T 1 
HETATM 48 H "H5'2" C2E . . . D 3 -20.364 -1.825 5.048 1 71.45 ? "H5'2" C2E 202 T 1 
HETATM 49 H H4' C2E . . . D 3 -23.131 -2.2 5.118 1 56.35 ? H4' C2E 202 T 1 
HETATM 50 H H3' C2E . . . D 3 -21.059 -0.349 5.448 1 50.85 ? H3' C2E 202 T 1 
HETATM 51 H H2' C2E . . . D 3 -21.727 0.895 7.029 1 45.08 ? H2' C2E 202 T 1 
HETATM 52 H HO2' C2E . . . D 3 -23.836 1.302 7.282 1 47.07 ? HO2' C2E 202 T 1 
HETATM 53 H H1' C2E . . . D 3 -23.365 -0.898 8.312 1 50.52 ? H1' C2E 202 T 1 
HETATM 54 H H8 C2E . . . D 3 -19.684 -1.288 7.528 1 50.09 ? H8 C2E 202 T 1 
HETATM 55 H HN1 C2E . . . D 3 -21.074 -1.877 13.514 1 55.75 ? HN1 C2E 202 T 1 
HETATM 56 H HN21 C2E . . . D 3 -23.43 -1.573 13.759 1 53.24 ? HN21 C2E 202 T 1 
HETATM 57 H HN22 C2E . . . D 3 -24.265 -1.296 12.568 1 53.24 ? HN22 C2E 202 T 1 
HETATM 58 H H511 C2E . . . D 3 -21.624 -1.426 1.906 1 54.54 ? H511 C2E 202 T 1 
HETATM 59 H H512 C2E . . . D 3 -20.987 -0.368 0.964 1 54.54 ? H512 C2E 202 T 1 
HETATM 60 H H4A C2E . . . D 3 -19.74 -2.477 0.891 1 52.45 ? H4A C2E 202 T 1 
HETATM 61 H H3A C2E . . . D 3 -18.972 -1.73 3.525 1 51.53 ? H3A C2E 202 T 1 
HETATM 62 H H2A C2E . . . D 3 -16.874 -2.597 3.053 1 58.18 ? H2A C2E 202 T 1 
HETATM 63 H HO2A C2E . . . D 3 -16.772 -4.224 1.829 1 60.1 ? HO2A C2E 202 T 1 
HETATM 64 H H1A C2E . . . D 3 -16.778 -1.502 0.659 1 56.77 ? H1A C2E 202 T 1 
HETATM 65 H H81 C2E . . . D 3 -18.287 0.784 3 1 50.46 ? H81 C2E 202 T 1 
HETATM 66 H HN11 C2E . . . D 3 -12.142 1.103 3.293 1 59.65 ? HN11 C2E 202 T 1 
HETATM 67 H HN24 C2E . . . D 3 -11.169 -0.659 2.013 1 60.99 ? HN24 C2E 202 T 1 
HETATM 68 H HN23 C2E . . . D 3 -12.027 -1.627 1.296 1 60.99 ? HN23 C2E 202 T 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           68 
#