data_5VX6
#
_model_server_result.job_id            V6PrMggNraRmW9ahN2EzUQ 
_model_server_result.datetime_utc      '2024-11-05 00:53:31' 
_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          5vx6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    5VX6 
#
_exptl.entry_id    5VX6 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            5VX6 
_cell.length_a            75.41 
_cell.length_b            75.41 
_cell.length_c            402.47 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VX6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C,D 1 1 
B,E,F 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 C N N 
? 2 D N N 
? 2 E N N 
? 2 F 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                     5VX6 
_atom_sites.fract_transf_matrix[1][1]    0.013261 
_atom_sites.fract_transf_matrix[1][2]    0.007656 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015312 
_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]    0.002485 
_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 A 1 301 219 C2E C2E . 
D 2 C2E A 1 302 220 C2E C2E . 
E 2 C2E B 1 301 219 C2E C2E . 
F 2 C2E B 1 302 220 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 . . . C 2 24.287 23.096 202.055 1 39.09 ? P1 C2E 301 A 1 
HETATM 2 O O2P C2E . . . C 2 23.977 21.636 202.289 1 28.54 ? O2P C2E 301 A 1 
HETATM 3 O O1P C2E . . . C 2 23.483 23.882 201.049 1 46.97 -1 O1P C2E 301 A 1 
HETATM 4 O O5' C2E . . . C 2 24.202 23.841 203.473 1 40.37 ? O5' C2E 301 A 1 
HETATM 5 C C5' C2E . . . C 2 24.31 22.989 204.601 1 53.96 ? C5' C2E 301 A 1 
HETATM 6 C C4' C2E . . . C 2 24.45 23.719 205.919 1 50.05 ? C4' C2E 301 A 1 
HETATM 7 O O4' C2E . . . C 2 23.179 23.682 206.567 1 48.07 ? O4' C2E 301 A 1 
HETATM 8 C C3' C2E . . . C 2 25.4 22.894 206.766 1 40.4 ? C3' C2E 301 A 1 
HETATM 9 O O3' C2E . . . C 2 26.641 23.562 206.963 1 50.1 ? O3' C2E 301 A 1 
HETATM 10 C C2' C2E . . . C 2 24.675 22.64 208.068 1 48.06 ? C2' C2E 301 A 1 
HETATM 11 O O2' C2E . . . C 2 25.096 23.587 209.055 1 44.38 ? O2' C2E 301 A 1 
HETATM 12 C C1' C2E . . . C 2 23.212 22.832 207.716 1 46.61 ? C1' C2E 301 A 1 
HETATM 13 N N9 C2E . . . C 2 22.68 21.497 207.334 1 44.3 ? N9 C2E 301 A 1 
HETATM 14 C C8 C2E . . . C 2 22.262 21.126 206.108 1 45.53 ? C8 C2E 301 A 1 
HETATM 15 N N7 C2E . . . C 2 21.843 19.841 206.081 1 48.65 ? N7 C2E 301 A 1 
HETATM 16 C C5 C2E . . . C 2 21.985 19.361 207.323 1 41.72 ? C5 C2E 301 A 1 
HETATM 17 C C6 C2E . . . C 2 21.723 18.07 207.987 1 45.1 ? C6 C2E 301 A 1 
HETATM 18 O O6 C2E . . . C 2 21.256 17.108 207.34 1 52.6 ? O6 C2E 301 A 1 
HETATM 19 N N1 C2E . . . C 2 22.004 17.972 209.293 1 49.41 ? N1 C2E 301 A 1 
HETATM 20 C C2 C2E . . . C 2 22.509 18.997 210.007 1 48.88 ? C2 C2E 301 A 1 
HETATM 21 N N2 C2E . . . C 2 22.766 18.814 211.327 1 56.4 ? N2 C2E 301 A 1 
HETATM 22 N N3 C2E . . . C 2 22.772 20.209 209.456 1 42.84 ? N3 C2E 301 A 1 
HETATM 23 C C4 C2E . . . C 2 22.535 20.448 208.145 1 42.99 ? C4 C2E 301 A 1 
HETATM 24 P P11 C2E . . . C 2 27.988 22.776 206.567 1 39.77 ? P11 C2E 301 A 1 
HETATM 25 O O21 C2E . . . C 2 27.974 21.457 207.305 1 30.95 ? O21 C2E 301 A 1 
HETATM 26 O O11 C2E . . . C 2 29.166 23.711 206.716 1 48.92 -1 O11 C2E 301 A 1 
HETATM 27 O O5A C2E . . . C 2 27.754 22.486 204.997 1 36.76 ? O5A C2E 301 A 1 
HETATM 28 C C5A C2E . . . C 2 28.332 23.354 204.023 1 36.72 ? C5A C2E 301 A 1 
HETATM 29 C C4A C2E . . . C 2 28.157 22.832 202.597 1 39.79 ? C4A C2E 301 A 1 
HETATM 30 O O4A C2E . . . C 2 29.05 21.733 202.387 1 40.76 ? O4A C2E 301 A 1 
HETATM 31 C C3A C2E . . . C 2 26.767 22.295 202.277 1 42.29 ? C3A C2E 301 A 1 
HETATM 32 O O3A C2E . . . C 2 25.859 23.244 201.719 1 42.43 ? O3A C2E 301 A 1 
HETATM 33 C C2A C2E . . . C 2 27.035 21.226 201.248 1 49.41 ? C2A C2E 301 A 1 
HETATM 34 O O2A C2E . . . C 2 27.03 21.833 199.954 1 42.69 ? O2A C2E 301 A 1 
HETATM 35 C C1A C2E . . . C 2 28.423 20.724 201.591 1 46.95 ? C1A C2E 301 A 1 
HETATM 36 N N91 C2E . . . C 2 28.242 19.486 202.385 1 37.91 ? N91 C2E 301 A 1 
HETATM 37 C C81 C2E . . . C 2 28.484 19.339 203.7 1 36.71 ? C81 C2E 301 A 1 
HETATM 38 N N71 C2E . . . C 2 28.197 18.074 204.105 1 32.72 ? N71 C2E 301 A 1 
HETATM 39 C C51 C2E . . . C 2 27.757 17.393 203.032 1 29.47 ? C51 C2E 301 A 1 
HETATM 40 C C61 C2E . . . C 2 27.287 16.017 202.752 1 32.84 ? C61 C2E 301 A 1 
HETATM 41 O O61 C2E . . . C 2 27.235 15.162 203.662 1 40.03 ? O61 C2E 301 A 1 
HETATM 42 N N11 C2E . . . C 2 26.922 15.72 201.497 1 39.9 ? N11 C2E 301 A 1 
HETATM 43 C C21 C2E . . . C 2 26.968 16.621 200.494 1 36.14 ? C21 C2E 301 A 1 
HETATM 44 N N21 C2E . . . C 2 26.581 16.248 199.247 1 43.25 ? N21 C2E 301 A 1 
HETATM 45 N N31 C2E . . . C 2 27.39 17.895 200.685 1 28.41 ? N31 C2E 301 A 1 
HETATM 46 C C41 C2E . . . C 2 27.787 18.329 201.903 1 31.38 ? C41 C2E 301 A 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           46 
#