data_7U3A
#
_model_server_result.job_id            ASHWeBXDkBnbG8AZnMpJNQ 
_model_server_result.datetime_utc      '2024-11-05 01:30:30' 
_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":"G","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 . . . G 2 46.629 47.04 57.038 1 38.97 ? P1 C2E 801 C 1 
HETATM 2 O O2P C2E . . . G 2 46.727 47.225 55.538 1 33.73 ? O2P C2E 801 C 1 
HETATM 3 O O1P C2E . . . G 2 46.794 45.555 57.253 1 42.29 ? O1P C2E 801 C 1 
HETATM 4 O O5' C2E . . . G 2 45.115 47.406 57.714 1 33.69 ? O5' C2E 801 C 1 
HETATM 5 C C5' C2E . . . G 2 44.316 48.466 57.138 1 31.95 ? C5' C2E 801 C 1 
HETATM 6 C C4' C2E . . . G 2 43.045 48.755 58.107 1 30.42 ? C4' C2E 801 C 1 
HETATM 7 O O4' C2E . . . G 2 41.934 47.669 57.867 1 26.49 ? O4' C2E 801 C 1 
HETATM 8 C C3' C2E . . . G 2 43.37 48.658 59.292 1 33.18 ? C3' C2E 801 C 1 
HETATM 9 O O3' C2E . . . G 2 43.581 50.036 59.886 1 39.5 ? O3' C2E 801 C 1 
HETATM 10 C C2' C2E . . . G 2 42.102 47.898 60.065 1 30.13 ? C2' C2E 801 C 1 
HETATM 11 O O2' C2E . . . G 2 41.068 48.876 60.417 1 30.5 ? O2' C2E 801 C 1 
HETATM 12 C C1' C2E . . . G 2 41.644 47.067 59.239 1 29.18 ? C1' C2E 801 C 1 
HETATM 13 N N9 C2E . . . G 2 42.362 45.734 59.387 1 36.16 ? N9 C2E 801 C 1 
HETATM 14 C C8 C2E . . . G 2 43.472 45.043 59.047 1 38.26 ? C8 C2E 801 C 1 
HETATM 15 N N7 C2E . . . G 2 43.384 43.814 59.609 1 38.34 ? N7 C2E 801 C 1 
HETATM 16 C C5 C2E . . . G 2 42.237 43.749 60.285 1 37.3 ? C5 C2E 801 C 1 
HETATM 17 C C6 C2E . . . G 2 41.598 42.623 61.116 1 34.15 ? C6 C2E 801 C 1 
HETATM 18 O O6 C2E . . . G 2 42.157 41.582 61.233 1 34.88 ? O6 C2E 801 C 1 
HETATM 19 N N1 C2E . . . G 2 40.327 42.83 61.747 1 30.98 ? N1 C2E 801 C 1 
HETATM 20 C C2 C2E . . . G 2 39.655 44.1 61.599 1 29.72 ? C2 C2E 801 C 1 
HETATM 21 N N2 C2E . . . G 2 38.36 44.317 62.242 1 28 ? N2 C2E 801 C 1 
HETATM 22 N N3 C2E . . . G 2 40.27 45.17 60.806 1 35.3 ? N3 C2E 801 C 1 
HETATM 23 C C4 C2E . . . G 2 41.595 44.948 60.148 1 37.81 ? C4 C2E 801 C 1 
HETATM 24 P P11 C2E . . . G 2 44.535 49.945 61.262 1 40.97 ? P11 C2E 801 C 1 
HETATM 25 O O21 C2E . . . G 2 45.019 51.248 61.865 1 47.94 ? O21 C2E 801 C 1 
HETATM 26 O O11 C2E . . . G 2 43.715 49.276 62.344 1 41.34 ? O11 C2E 801 C 1 
HETATM 27 O O5A C2E . . . G 2 45.707 48.845 60.76 1 40.41 ? O5A C2E 801 C 1 
HETATM 28 C C5A C2E . . . G 2 46.879 49.553 60.391 1 41.4 ? C5A C2E 801 C 1 
HETATM 29 C C4A C2E . . . G 2 48.046 48.633 60.365 1 43.29 ? C4A C2E 801 C 1 
HETATM 30 O O4A C2E . . . G 2 48.24 48.086 61.526 1 49.43 ? O4A C2E 801 C 1 
HETATM 31 C C3A C2E . . . G 2 47.756 47.32 59.355 1 41.27 ? C3A C2E 801 C 1 
HETATM 32 O O3A C2E . . . G 2 47.887 47.744 57.907 1 41.88 ? O3A C2E 801 C 1 
HETATM 33 C C2A C2E . . . G 2 48.602 46.486 59.649 1 40.7 ? C2A C2E 801 C 1 
HETATM 34 O O2A C2E . . . G 2 49.795 46.611 58.732 1 37.95 ? O2A C2E 801 C 1 
HETATM 35 C C1A C2E . . . G 2 49.036 46.845 61.176 1 45.83 ? C1A C2E 801 C 1 
HETATM 36 N N91 C2E . . . G 2 48.894 45.777 61.964 1 43.98 ? N91 C2E 801 C 1 
HETATM 37 C C81 C2E . . . G 2 47.823 46.345 62.565 1 44.58 ? C81 C2E 801 C 1 
HETATM 38 N N71 C2E . . . G 2 47.376 45.482 63.504 1 42.62 ? N71 C2E 801 C 1 
HETATM 39 C C51 C2E . . . G 2 48.157 44.401 63.476 1 41.47 ? C51 C2E 801 C 1 
HETATM 40 C C61 C2E . . . G 2 48.146 43.101 64.292 1 36.39 ? C61 C2E 801 C 1 
HETATM 41 O O61 C2E . . . G 2 47.326 42.927 65.135 1 30.76 ? O61 C2E 801 C 1 
HETATM 42 N N11 C2E . . . G 2 49.132 42.098 64.034 1 44.07 ? N11 C2E 801 C 1 
HETATM 43 C C21 C2E . . . G 2 50.131 42.298 63.014 1 52.51 ? C21 C2E 801 C 1 
HETATM 44 N N21 C2E . . . G 2 51.135 41.265 62.757 1 58.98 ? N21 C2E 801 C 1 
HETATM 45 N N31 C2E . . . G 2 50.136 43.539 62.24 1 47.88 ? N31 C2E 801 C 1 
HETATM 46 C C41 C2E . . . G 2 49.107 44.586 62.51 1 43.61 ? C41 C2E 801 C 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           46 
#