data_7U3A
#
_model_server_result.job_id            YxCIzj99UoBjsC7kp1Z5-w 
_model_server_result.datetime_utc      '2024-11-05 01:25:23' 
_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          7u3a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":801}' 
#
_entry.id    7U3A 
#
_exptl.entry_id    7U3A 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          93.73 
_cell.angle_gamma         90 
_cell.entry_id            7U3A 
_cell.length_a            129.47 
_cell.length_b            127.66 
_cell.length_c            179.72 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7U3A 
_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 dimeric 2 author_and_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,E,F 1 1 
C,D,G,H 2 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
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H 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                     7U3A 
_atom_sites.fract_transf_matrix[1][1]    0.007724 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000504 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007833 
_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]    0.005576 
_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
E 2 C2E A 1 801 201 C2E C2E . 
F 2 C2E B 1 801 201 C2E C2E . 
G 2 C2E C 1 801 201 C2E C2E . 
H 2 C2E D 1 801 201 C2E C2E . 
#
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 . . . H 2 81.906 -2.343 63.443 1 41.64 ? P1 C2E 801 D 1 
HETATM 2 O O2P C2E . . . H 2 82.175 -2.302 61.952 1 37.31 ? O2P C2E 801 D 1 
HETATM 3 O O1P C2E . . . H 2 81.612 -0.909 63.81 1 47.09 ? O1P C2E 801 D 1 
HETATM 4 O O5' C2E . . . H 2 83.261 -2.752 64.383 1 37.75 ? O5' C2E 801 D 1 
HETATM 5 C C5' C2E . . . H 2 83.704 -4.13 64.412 1 41.63 ? C5' C2E 801 D 1 
HETATM 6 C C4' C2E . . . H 2 84.673 -4.38 65.693 1 47.06 ? C4' C2E 801 D 1 
HETATM 7 O O4' C2E . . . H 2 85.92 -3.425 65.633 1 49.36 ? O4' C2E 801 D 1 
HETATM 8 C C3' C2E . . . H 2 84.079 -4.11 66.738 1 44.18 ? C3' C2E 801 D 1 
HETATM 9 O O3' C2E . . . H 2 83.628 -5.383 67.423 1 47.69 ? O3' C2E 801 D 1 
HETATM 10 C C2' C2E . . . H 2 85.166 -3.321 67.725 1 40.32 ? C2' C2E 801 D 1 
HETATM 11 O O2' C2E . . . H 2 85.917 -4.299 68.52 1 41.89 ? O2' C2E 801 D 1 
HETATM 12 C C1' C2E . . . H 2 85.942 -2.683 66.968 1 41.89 ? C1' C2E 801 D 1 
HETATM 13 N N9 C2E . . . H 2 85.438 -1.259 66.78 1 43.25 ? N9 C2E 801 D 1 
HETATM 14 C C8 C2E . . . H 2 84.767 -0.433 65.948 1 44.25 ? C8 C2E 801 D 1 
HETATM 15 N N7 C2E . . . H 2 84.723 0.791 66.526 1 45.73 ? N7 C2E 801 D 1 
HETATM 16 C C5 C2E . . . H 2 85.359 0.72 67.696 1 44.46 ? C5 C2E 801 D 1 
HETATM 17 C C6 C2E . . . H 2 85.632 1.774 68.783 1 46.71 ? C6 C2E 801 D 1 
HETATM 18 O O6 C2E . . . H 2 85.241 2.887 68.641 1 56.89 ? O6 C2E 801 D 1 
HETATM 19 N N1 C2E . . . H 2 86.357 1.414 69.965 1 40.89 ? N1 C2E 801 D 1 
HETATM 20 C C2 C2E . . . H 2 86.829 0.06 70.13 1 41.66 ? C2 C2E 801 D 1 
HETATM 21 N N2 C2E . . . H 2 87.57 -0.316 71.335 1 41.97 ? N2 C2E 801 D 1 
HETATM 22 N N3 C2E . . . H 2 86.565 -0.94 69.09 1 43.38 ? N3 C2E 801 D 1 
HETATM 23 C C4 C2E . . . H 2 85.807 -0.561 67.857 1 43.4 ? C4 C2E 801 D 1 
HETATM 24 P P11 C2E . . . H 2 82.354 -5.051 68.458 1 51.57 ? P11 C2E 801 D 1 
HETATM 25 O O21 C2E . . . H 2 81.7 -6.22 69.164 1 57.2 ? O21 C2E 801 D 1 
HETATM 26 O O11 C2E . . . H 2 82.865 -4.133 69.554 1 62.13 ? O11 C2E 801 D 1 
HETATM 27 O O5A C2E . . . H 2 81.399 -4.115 67.441 1 38.5 ? O5A C2E 801 D 1 
HETATM 28 C C5A C2E . . . H 2 80.677 -4.952 66.555 1 39.4 ? C5A C2E 801 D 1 
HETATM 29 C C4A C2E . . . H 2 79.518 -4.177 66.058 1 49.4 ? C4A C2E 801 D 1 
HETATM 30 O O4A C2E . . . H 2 78.851 -3.711 67.065 1 63.84 ? O4A C2E 801 D 1 
HETATM 31 C C3A C2E . . . H 2 80.06 -2.803 65.257 1 43.81 ? C3A C2E 801 D 1 
HETATM 32 O O3A C2E . . . H 2 80.509 -3.19 63.862 1 41.05 ? O3A C2E 801 D 1 
HETATM 33 C C2A C2E . . . H 2 79.105 -2.036 65.246 1 49.43 ? C2A C2E 801 D 1 
HETATM 34 O O2A C2E . . . H 2 78.304 -2.208 63.978 1 53.22 ? O2A C2E 801 D 1 
HETATM 35 C C1A C2E . . . H 2 78.204 -2.448 66.543 1 59.43 ? C1A C2E 801 D 1 
HETATM 36 N N91 C2E . . . H 2 78.089 -1.396 67.364 1 57.94 ? N91 C2E 801 D 1 
HETATM 37 C C81 C2E . . . H 2 78.811 -1.997 68.353 1 56.53 ? C81 C2E 801 D 1 
HETATM 38 N N71 C2E . . . H 2 78.883 -1.113 69.379 1 58.04 ? N71 C2E 801 D 1 
HETATM 39 C C51 C2E . . . H 2 78.217 -0.004 69.039 1 56.85 ? C51 C2E 801 D 1 
HETATM 40 C C61 C2E . . . H 2 77.944 1.312 69.782 1 56.53 ? C61 C2E 801 D 1 
HETATM 41 O O61 C2E . . . H 2 78.367 1.482 70.879 1 61.05 ? O61 C2E 801 D 1 
HETATM 42 N N11 C2E . . . H 2 77.175 2.34 69.147 1 50.85 ? N11 C2E 801 D 1 
HETATM 43 C C21 C2E . . . H 2 76.658 2.142 67.815 1 49.51 ? C21 C2E 801 D 1 
HETATM 44 N N21 C2E . . . H 2 75.875 3.195 67.168 1 49.42 ? N21 C2E 801 D 1 
HETATM 45 N N31 C2E . . . H 2 76.921 0.883 67.116 1 52.41 ? N31 C2E 801 D 1 
HETATM 46 C C41 C2E . . . H 2 77.721 -0.188 67.779 1 56.23 ? C41 C2E 801 D 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           46 
#