data_6S86
#
_model_server_result.job_id            LGlQauV0SNGDGxWSbvgNWw 
_model_server_result.datetime_utc      '2024-11-25 08:47:15' 
_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          6s86 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    6S86 
#
_exptl.entry_id    6S86 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              690.411 
_entity.id                          2 
_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    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            6S86 
_cell.length_a            110.693 
_cell.length_b            110.693 
_cell.length_c            34.327 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6S86 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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                     6S86 
_atom_sites.fract_transf_matrix[1][1]    0.009034 
_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]    0.009034 
_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]    0.029132 
_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 2 C2E B 1 401 401 C2E C2E . 
D 3 HOH A 1 401 3 HOH HOH . 
D 3 HOH A 2 402 33 HOH HOH . 
D 3 HOH A 3 403 38 HOH HOH . 
D 3 HOH A 4 404 25 HOH HOH . 
D 3 HOH A 5 405 8 HOH HOH . 
D 3 HOH A 6 406 11 HOH HOH . 
D 3 HOH A 7 407 34 HOH HOH . 
D 3 HOH A 8 408 37 HOH HOH . 
D 3 HOH A 9 409 5 HOH HOH . 
D 3 HOH A 10 410 2 HOH HOH . 
D 3 HOH A 11 411 13 HOH HOH . 
D 3 HOH A 12 412 28 HOH HOH . 
D 3 HOH A 13 413 27 HOH HOH . 
D 3 HOH A 14 414 23 HOH HOH . 
E 3 HOH B 1 501 32 HOH HOH . 
E 3 HOH B 2 502 22 HOH HOH . 
E 3 HOH B 3 503 31 HOH HOH . 
E 3 HOH B 4 504 9 HOH HOH . 
E 3 HOH B 5 505 1 HOH HOH . 
E 3 HOH B 6 506 39 HOH HOH . 
E 3 HOH B 7 507 4 HOH HOH . 
E 3 HOH B 8 508 17 HOH HOH . 
E 3 HOH B 9 509 29 HOH HOH . 
E 3 HOH B 10 510 26 HOH HOH . 
E 3 HOH B 11 511 36 HOH HOH . 
E 3 HOH B 12 512 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 P1 C2E . . . C 2 20.371 33.062 -2.133 1 42.09 ? P1 C2E 401 B 1 
HETATM 2 O O2P C2E . . . C 2 18.996 33.645 -2.361 1 41.23 ? O2P C2E 401 B 1 
HETATM 3 O O1P C2E . . . C 2 20.818 32.201 -3.285 1 46.14 ? O1P C2E 401 B 1 
HETATM 4 O O5' C2E . . . C 2 21.377 34.296 -1.981 1 39.39 ? O5' C2E 401 B 1 
HETATM 5 C C5' C2E . . . C 2 22.7 34.011 -1.592 1 38.66 ? C5' C2E 401 B 1 
HETATM 6 C C4' C2E . . . C 2 23.326 35.287 -1.1 1 38.09 ? C4' C2E 401 B 1 
HETATM 7 O O4' C2E . . . C 2 23.102 36.357 -2.04 1 37.19 ? O4' C2E 401 B 1 
HETATM 8 C C3' C2E . . . C 2 22.79 35.818 0.233 1 38.75 ? C3' C2E 401 B 1 
HETATM 9 O O3' C2E . . . C 2 23.321 35.226 1.38 1 40.7 ? O3' C2E 401 B 1 
HETATM 10 C C2' C2E . . . C 2 23.203 37.299 0.148 1 38.12 ? C2' C2E 401 B 1 
HETATM 11 O O2' C2E . . . C 2 24.571 37.454 0.487 1 40.89 ? O2' C2E 401 B 1 
HETATM 12 C C1' C2E . . . C 2 22.959 37.597 -1.332 1 36.95 ? C1' C2E 401 B 1 
HETATM 13 N N9 C2E . . . C 2 21.592 38.133 -1.394 1 38.63 ? N9 C2E 401 B 1 
HETATM 14 C C8 C2E . . . C 2 20.476 37.429 -1.639 1 39.33 ? C8 C2E 401 B 1 
HETATM 15 N N7 C2E . . . C 2 19.394 38.25 -1.596 1 40.34 ? N7 C2E 401 B 1 
HETATM 16 C C5 C2E . . . C 2 19.832 39.489 -1.303 1 39.78 ? C5 C2E 401 B 1 
HETATM 17 C C6 C2E . . . C 2 19.225 40.822 -1.105 1 41.91 ? C6 C2E 401 B 1 
HETATM 18 O O6 C2E . . . C 2 17.989 40.968 -1.21 1 44.82 ? O6 C2E 401 B 1 
HETATM 19 N N1 C2E . . . C 2 20.026 41.858 -0.813 1 42.81 ? N1 C2E 401 B 1 
HETATM 20 C C2 C2E . . . C 2 21.361 41.717 -0.696 1 40.07 ? C2 C2E 401 B 1 
HETATM 21 N N2 C2E . . . C 2 22.104 42.812 -0.398 1 38.81 ? N2 C2E 401 B 1 
HETATM 22 N N3 C2E . . . C 2 21.99 40.525 -0.863 1 39.03 ? N3 C2E 401 B 1 
HETATM 23 C C4 C2E . . . C 2 21.286 39.406 -1.161 1 38.42 ? C4 C2E 401 B 1 
HETATM 24 P P11 C2E . . . C 2 22.365 35.296 2.674 1 35.93 ? P11 C2E 401 B 1 
HETATM 25 O O21 C2E . . . C 2 21.797 36.684 2.857 1 36.67 ? O21 C2E 401 B 1 
HETATM 26 O O11 C2E . . . C 2 23.192 34.872 3.861 1 37.85 ? O11 C2E 401 B 1 
HETATM 27 O O5A C2E . . . C 2 21.154 34.271 2.47 1 37.12 ? O5A C2E 401 B 1 
HETATM 28 C C5A C2E . . . C 2 21.498 32.931 2.194 1 39.51 ? C5A C2E 401 B 1 
HETATM 29 C C4A C2E . . . C 2 20.289 32.191 1.688 1 40.73 ? C4A C2E 401 B 1 
HETATM 30 O O4A C2E . . . C 2 19.17 32.336 2.59 1 39.6 ? O4A C2E 401 B 1 
HETATM 31 C C3A C2E . . . C 2 19.764 32.655 0.32 1 42.82 ? C3A C2E 401 B 1 
HETATM 32 O O3A C2E . . . C 2 20.424 32.147 -0.803 1 47.3 ? O3A C2E 401 B 1 
HETATM 33 C C2A C2E . . . C 2 18.31 32.148 0.382 1 43.76 ? C2A C2E 401 B 1 
HETATM 34 O O2A C2E . . . C 2 18.248 30.765 0.057 1 46.7 ? O2A C2E 401 B 1 
HETATM 35 C C1A C2E . . . C 2 17.941 32.391 1.848 1 41.12 ? C1A C2E 401 B 1 
HETATM 36 N N91 C2E . . . C 2 17.319 33.722 1.898 1 41.21 ? N91 C2E 401 B 1 
HETATM 37 C C81 C2E . . . C 2 17.945 34.878 2.176 1 40.4 ? C81 C2E 401 B 1 
HETATM 38 N N71 C2E . . . C 2 17.064 35.91 2.115 1 40.42 ? N71 C2E 401 B 1 
HETATM 39 C C51 C2E . . . C 2 15.86 35.409 1.781 1 41.69 ? C51 C2E 401 B 1 
HETATM 40 C C61 C2E . . . C 2 14.501 35.946 1.548 1 43.91 ? C61 C2E 401 B 1 
HETATM 41 O O61 C2E . . . C 2 14.274 37.168 1.656 1 45.55 ? O61 C2E 401 B 1 
HETATM 42 N N11 C2E . . . C 2 13.524 35.088 1.22 1 45.89 ? N11 C2E 401 B 1 
HETATM 43 C C21 C2E . . . C 2 13.744 33.764 1.098 1 45.1 ? C21 C2E 401 B 1 
HETATM 44 N N21 C2E . . . C 2 12.701 32.967 0.761 1 45.36 ? N21 C2E 401 B 1 
HETATM 45 N N31 C2E . . . C 2 14.965 33.199 1.296 1 42.63 ? N31 C2E 401 B 1 
HETATM 46 C C41 C2E . . . C 2 16.035 33.96 1.633 1 41.95 ? C41 C2E 401 B 1 
HETATM 47 H "H5'1" C2E . . . C 2 22.705 33.261 -0.799 1 46.39 ? "H5'1" C2E 401 B 1 
HETATM 48 H "H5'2" C2E . . . C 2 23.264 33.62 -2.441 1 46.39 ? "H5'2" C2E 401 B 1 
HETATM 49 H H4' C2E . . . C 2 24.407 35.119 -0.992 1 45.71 ? H4' C2E 401 B 1 
HETATM 50 H H3' C2E . . . C 2 21.693 35.747 0.238 1 46.5 ? H3' C2E 401 B 1 
HETATM 51 H H2' C2E . . . C 2 22.552 37.916 0.783 1 45.74 ? H2' C2E 401 B 1 
HETATM 52 H HO2' C2E . . . C 2 24.836 38.373 0.345 1 49.07 ? HO2' C2E 401 B 1 
HETATM 53 H H1' C2E . . . C 2 23.688 38.339 -1.686 1 44.34 ? H1' C2E 401 B 1 
HETATM 54 H H8 C2E . . . C 2 20.439 36.371 -1.856 1 47.2 ? H8 C2E 401 B 1 
HETATM 55 H HN1 C2E . . . C 2 19.602 42.796 -0.673 1 51.37 ? HN1 C2E 401 B 1 
HETATM 56 H HN21 C2E . . . C 2 23.106 42.733 -0.305 1 46.57 ? HN21 C2E 401 B 1 
HETATM 57 H HN22 C2E . . . C 2 21.654 43.706 -0.27 1 46.57 ? HN22 C2E 401 B 1 
HETATM 58 H H511 C2E . . . C 2 22.291 32.9 1.444 1 47.41 ? H511 C2E 401 B 1 
HETATM 59 H H512 C2E . . . C 2 21.87 32.452 3.102 1 47.41 ? H512 C2E 401 B 1 
HETATM 60 H H4A C2E . . . C 2 20.552 31.127 1.608 1 48.88 ? H4A C2E 401 B 1 
HETATM 61 H H3A C2E . . . C 2 19.759 33.754 0.292 1 51.38 ? H3A C2E 401 B 1 
HETATM 62 H H2A C2E . . . C 2 17.67 32.748 -0.28 1 52.51 ? H2A C2E 401 B 1 
HETATM 63 H HO2A C2E . . . C 2 17.358 30.432 0.232 1 56.04 ? HO2A C2E 401 B 1 
HETATM 64 H H1A C2E . . . C 2 17.24 31.616 2.189 1 49.34 ? H1A C2E 401 B 1 
HETATM 65 H H81 C2E . . . C 2 18.992 34.977 2.424 1 48.48 ? H81 C2E 401 B 1 
HETATM 66 H HN11 C2E . . . C 2 12.566 35.458 1.054 1 55.07 ? HN11 C2E 401 B 1 
HETATM 67 H HN24 C2E . . . C 2 11.787 33.369 0.61 1 54.43 ? HN24 C2E 401 B 1 
HETATM 68 H HN23 C2E . . . C 2 12.838 31.971 0.662 1 54.43 ? HN23 C2E 401 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           68 
#