data_6PFJ
#
_model_server_result.job_id            KIkdi_i9o_zuRaS-kT2kPQ 
_model_server_result.datetime_utc      '2024-12-27 01:43:38' 
_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":"C","auth_seq_id":201}' 
#
_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 . . . C 3 -9.351 2.259 4.239 1 59.9 ? P1 C2E 201 T 1 
HETATM 2 O O2P C2E . . . C 3 -7.91 2.138 3.906 1 70.11 ? O2P C2E 201 T 1 
HETATM 3 O O1P C2E . . . C 3 -10.473 1.951 3.334 1 52.45 ? O1P C2E 201 T 1 
HETATM 4 O O5' C2E . . . C 3 -9.511 3.761 4.761 1 62.73 ? O5' C2E 201 T 1 
HETATM 5 C C5' C2E . . . C 3 -10.394 4.367 4.344 1 58.5 ? C5' C2E 201 T 1 
HETATM 6 C C4' C2E . . . C 3 -10.406 5.773 4.989 1 59.57 ? C4' C2E 201 T 1 
HETATM 7 O O4' C2E . . . C 3 -10.358 6.709 3.899 1 47.83 ? O4' C2E 201 T 1 
HETATM 8 C C3' C2E . . . C 3 -11.771 5.922 5.705 1 54.2 ? C3' C2E 201 T 1 
HETATM 9 O O3' C2E . . . C 3 -11.678 6.206 7.095 1 59.94 ? O3' C2E 201 T 1 
HETATM 10 C C2' C2E . . . C 3 -12.466 7.042 4.93 1 51.13 ? C2' C2E 201 T 1 
HETATM 11 O O2' C2E . . . C 3 -12.278 8.271 5.525 1 56.21 ? O2' C2E 201 T 1 
HETATM 12 C C1' C2E . . . C 3 -11.694 7.122 3.6 1 55.36 ? C1' C2E 201 T 1 
HETATM 13 N N9 C2E . . . C 3 -12.223 6.173 2.5 1 51.51 ? N9 C2E 201 T 1 
HETATM 14 C C8 C2E . . . C 3 -12.625 4.812 2.554 1 47.65 ? C8 C2E 201 T 1 
HETATM 15 N N7 C2E . . . C 3 -12.94 4.324 1.346 1 51.02 ? N7 C2E 201 T 1 
HETATM 16 C C5 C2E . . . C 3 -12.753 5.398 0.482 1 47.94 ? C5 C2E 201 T 1 
HETATM 17 C C6 C2E . . . C 3 -12.935 5.458 -0.898 1 47.52 ? C6 C2E 201 T 1 
HETATM 18 O O6 C2E . . . C 3 -13.317 4.64 -1.716 1 50.47 ? O6 C2E 201 T 1 
HETATM 19 N N1 C2E . . . C 3 -12.624 6.741 -1.409 1 47.3 ? N1 C2E 201 T 1 
HETATM 20 C C2 C2E . . . C 3 -12.194 7.759 -0.603 1 51.29 ? C2 C2E 201 T 1 
HETATM 21 N N2 C2E . . . C 3 -11.94 8.967 -1.233 1 51.38 ? N2 C2E 201 T 1 
HETATM 22 N N3 C2E . . . C 3 -12.007 7.714 0.713 1 48.27 ? N3 C2E 201 T 1 
HETATM 23 C C4 C2E . . . C 3 -12.309 6.531 1.206 1 48.63 ? C4 C2E 201 T 1 
HETATM 24 P P11 C2E . . . C 3 -12.595 5.397 8.184 1 57.14 ? P11 C2E 201 T 1 
HETATM 25 O O21 C2E . . . C 3 -12.145 5.62 9.582 1 59.64 ? O21 C2E 201 T 1 
HETATM 26 O O11 C2E . . . C 3 -14.018 5.505 7.718 1 52.07 ? O11 C2E 201 T 1 
HETATM 27 O O5A C2E . . . C 3 -12.094 3.869 7.711 1 52.14 ? O5A C2E 201 T 1 
HETATM 28 C C5A C2E . . . C 3 -10.958 3.318 8.283 1 59.52 ? C5A C2E 201 T 1 
HETATM 29 C C4A C2E . . . C 3 -10.756 1.843 7.847 1 55.46 ? C4A C2E 201 T 1 
HETATM 30 O O4A C2E . . . C 3 -11.796 1.053 8.407 1 56.73 ? O4A C2E 201 T 1 
HETATM 31 C C3A C2E . . . C 3 -10.83 1.628 6.33 1 58.38 ? C3A C2E 201 T 1 
HETATM 32 O O3A C2E . . . C 3 -9.571 1.722 5.744 1 58.51 ? O3A C2E 201 T 1 
HETATM 33 C C2A C2E . . . C 3 -11.282 0.181 6.245 1 50.77 ? C2A C2E 201 T 1 
HETATM 34 O O2A C2E . . . C 3 -10.159 -0.606 6.433 1 57.26 ? O2A C2E 201 T 1 
HETATM 35 C C1A C2E . . . C 3 -12.142 0.054 7.475 1 58.49 ? C1A C2E 201 T 1 
HETATM 36 N N91 C2E . . . C 3 -13.595 0.282 7.171 1 54.37 ? N91 C2E 201 T 1 
HETATM 37 C C81 C2E . . . C 3 -14.387 1.471 7.339 1 52.82 ? C81 C2E 201 T 1 
HETATM 38 N N71 C2E . . . C 3 -15.678 1.28 7.015 1 50.51 ? N71 C2E 201 T 1 
HETATM 39 C C51 C2E . . . C 3 -15.724 -0.04 6.6 1 50.61 ? C51 C2E 201 T 1 
HETATM 40 C C61 C2E . . . C 3 -16.87 -0.784 6.123 1 45.6 ? C61 C2E 201 T 1 
HETATM 41 O O61 C2E . . . C 3 -18.046 -0.447 5.963 1 41.69 ? O61 C2E 201 T 1 
HETATM 42 N N11 C2E . . . C 3 -16.533 -2.083 5.805 1 44.98 ? N11 C2E 201 T 1 
HETATM 43 C C21 C2E . . . C 3 -15.192 -2.578 5.977 1 50.34 ? C21 C2E 201 T 1 
HETATM 44 N N21 C2E . . . C 3 -14.998 -3.832 5.643 1 53.74 ? N21 C2E 201 T 1 
HETATM 45 N N31 C2E . . . C 3 -14.094 -1.903 6.393 1 52.84 ? N31 C2E 201 T 1 
HETATM 46 C C41 C2E . . . C 3 -14.415 -0.643 6.694 1 50.63 ? C41 C2E 201 T 1 
HETATM 47 H "H5'1" C2E . . . C 3 -10.335 4.43 3.378 1 70.17 ? "H5'1" C2E 201 T 1 
HETATM 48 H "H5'2" C2E . . . C 3 -11.221 3.897 4.531 1 70.17 ? "H5'2" C2E 201 T 1 
HETATM 49 H H4' C2E . . . C 3 -9.637 5.922 5.561 1 71.46 ? H4' C2E 201 T 1 
HETATM 50 H H3' C2E . . . C 3 -12.286 5.118 5.537 1 65.01 ? H3' C2E 201 T 1 
HETATM 51 H H2' C2E . . . C 3 -13.403 6.828 4.8 1 61.33 ? H2' C2E 201 T 1 
HETATM 52 H HO2' C2E . . . C 3 -13.015 8.69 5.45 1 67.42 ? HO2' C2E 201 T 1 
HETATM 53 H H1' C2E . . . C 3 -11.682 8.021 3.235 1 66.4 ? H1' C2E 201 T 1 
HETATM 54 H H8 C2E . . . C 3 -12.627 4.337 3.354 1 57.15 ? H8 C2E 201 T 1 
HETATM 55 H HN1 C2E . . . C 3 -12.727 6.871 -2.253 1 56.73 ? HN1 C2E 201 T 1 
HETATM 56 H HN21 C2E . . . C 3 -11.649 9.65 -0.8 1 61.63 ? HN21 C2E 201 T 1 
HETATM 57 H HN22 C2E . . . C 3 -12.04 9.028 -2.085 1 61.63 ? HN22 C2E 201 T 1 
HETATM 58 H H511 C2E . . . C 3 -11.017 3.387 9.249 1 71.4 ? H511 C2E 201 T 1 
HETATM 59 H H512 C2E . . . C 3 -10.191 3.861 8.042 1 71.4 ? H512 C2E 201 T 1 
HETATM 60 H H4A C2E . . . C 3 -9.928 1.495 8.214 1 66.52 ? H4A C2E 201 T 1 
HETATM 61 H H3A C2E . . . C 3 -11.502 2.198 5.924 1 70.03 ? H3A C2E 201 T 1 
HETATM 62 H H2A C2E . . . C 3 -11.755 0.011 5.415 1 60.9 ? H2A C2E 201 T 1 
HETATM 63 H HO2A C2E . . . C 3 -10.409 -1.411 6.326 1 68.68 ? HO2A C2E 201 T 1 
HETATM 64 H H1A C2E . . . C 3 -12.069 -0.817 7.897 1 70.15 ? H1A C2E 201 T 1 
HETATM 65 H H81 C2E . . . C 3 -14.017 2.257 7.672 1 63.35 ? H81 C2E 201 T 1 
HETATM 66 H HN11 C2E . . . C 3 -17.155 -2.6 5.514 1 53.94 ? HN11 C2E 201 T 1 
HETATM 67 H HN24 C2E . . . C 3 -14.224 -4.202 5.702 1 64.45 ? HN24 C2E 201 T 1 
HETATM 68 H HN23 C2E . . . C 3 -15.657 -4.3 5.348 1 64.45 ? HN23 C2E 201 T 1 
#
_model_server_stats.io_time_ms              76 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           68 
#