data_3KLO
#
_model_server_result.job_id            '_QG21lh4J3Y5CjL5Pj3Zfw' 
_model_server_result.datetime_utc      '2024-12-20 05:42:48' 
_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          3klo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":225}' 
#
_entry.id    3KLO 
#
_exptl.entry_id    3KLO 
_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         90 
_cell.entry_id            3KLO 
_cell.length_a            121.703 
_cell.length_b            121.703 
_cell.length_c            208.227 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KLO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 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 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,E,K 1 1 
B,F,G,L 1 2 
C,H,M 2 1 
D,I,J,N 2 3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_455 -y-1/2,x+1/2,z+1/4 0 -1 0 1 0 0 0 0 1 -60.8515 60.8515 52.05675 
3 'crystal symmetry operation' 4_444 y-1/2,-x-1/2,z-1/4 0 1 0 -1 0 0 0 0 1 -60.8515 -60.8515 -52.05675 
#
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 H N N 
? 2 I 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                     3KLO 
_atom_sites.fract_transf_matrix[1][1]    0.008217 
_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]    0.008217 
_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]    0.004802 
_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 1 225 1 C2E C2E . 
F 2 C2E B 1 225 3 C2E C2E . 
G 3 TAR B 1 226 1 TAR TAR . 
H 2 C2E C 1 225 2 C2E C2E . 
I 2 C2E D 1 225 4 C2E C2E . 
J 3 TAR D 1 226 2 TAR TAR . 
K 4 HOH A 1 226 1 HOH HOH . 
K 4 HOH A 2 227 2 HOH HOH . 
K 4 HOH A 3 228 3 HOH HOH . 
K 4 HOH A 4 229 4 HOH HOH . 
K 4 HOH A 5 230 5 HOH HOH . 
K 4 HOH A 6 231 6 HOH HOH . 
K 4 HOH A 7 232 7 HOH HOH . 
K 4 HOH A 8 233 8 HOH HOH . 
K 4 HOH A 9 234 9 HOH HOH . 
K 4 HOH A 10 235 10 HOH HOH . 
K 4 HOH A 11 236 25 HOH HOH . 
K 4 HOH A 12 237 32 HOH HOH . 
L 4 HOH B 1 227 11 HOH HOH . 
L 4 HOH B 2 228 12 HOH HOH . 
L 4 HOH B 3 229 13 HOH HOH . 
L 4 HOH B 4 230 14 HOH HOH . 
L 4 HOH B 5 231 15 HOH HOH . 
L 4 HOH B 6 232 16 HOH HOH . 
L 4 HOH B 7 233 17 HOH HOH . 
L 4 HOH B 8 234 18 HOH HOH . 
L 4 HOH B 9 235 19 HOH HOH . 
L 4 HOH B 10 236 20 HOH HOH . 
L 4 HOH B 11 237 21 HOH HOH . 
L 4 HOH B 12 238 22 HOH HOH . 
L 4 HOH B 13 239 23 HOH HOH . 
L 4 HOH B 14 240 24 HOH HOH . 
L 4 HOH B 15 241 26 HOH HOH . 
L 4 HOH B 16 242 27 HOH HOH . 
L 4 HOH B 17 243 28 HOH HOH . 
L 4 HOH B 18 244 29 HOH HOH . 
L 4 HOH B 19 245 30 HOH HOH . 
M 4 HOH C 1 226 31 HOH HOH . 
M 4 HOH C 2 227 33 HOH HOH . 
M 4 HOH C 3 228 34 HOH HOH . 
M 4 HOH C 4 229 36 HOH HOH . 
M 4 HOH C 5 230 37 HOH HOH . 
M 4 HOH C 6 231 38 HOH HOH . 
M 4 HOH C 7 232 49 HOH HOH . 
N 4 HOH D 1 227 35 HOH HOH . 
N 4 HOH D 2 228 39 HOH HOH . 
N 4 HOH D 3 229 40 HOH HOH . 
N 4 HOH D 4 230 41 HOH HOH . 
N 4 HOH D 5 231 42 HOH HOH . 
N 4 HOH D 6 232 43 HOH HOH . 
N 4 HOH D 7 233 44 HOH HOH . 
N 4 HOH D 8 234 46 HOH HOH . 
N 4 HOH D 9 235 47 HOH HOH . 
N 4 HOH D 10 236 48 HOH HOH . 
N 4 HOH D 11 237 50 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 . . . I 2 -49.061 5.006 41.812 1 43.41 ? P1 C2E 225 D 1 
HETATM 2 O O2P C2E . . . I 2 -48.111 6.287 41.554 1 46.14 ? O2P C2E 225 D 1 
HETATM 3 O O1P C2E . . . I 2 -48.272 3.76 41.8 1 48 ? O1P C2E 225 D 1 
HETATM 4 O O5' C2E . . . I 2 -50.198 4.982 40.679 1 48.63 ? O5' C2E 225 D 1 
HETATM 5 C C5' C2E . . . I 2 -51.122 6.068 40.51 1 47.81 ? C5' C2E 225 D 1 
HETATM 6 C C4' C2E . . . I 2 -52.415 5.605 39.823 1 50.24 ? C4' C2E 225 D 1 
HETATM 7 O O4' C2E . . . I 2 -52.162 4.889 38.601 1 51.65 ? O4' C2E 225 D 1 
HETATM 8 C C3' C2E . . . I 2 -53.207 4.628 40.703 1 49.3 ? C3' C2E 225 D 1 
HETATM 9 O O3' C2E . . . I 2 -53.994 5.253 41.71 1 47.69 ? O3' C2E 225 D 1 
HETATM 10 C C2' C2E . . . I 2 -54.053 3.871 39.668 1 49.82 ? C2' C2E 225 D 1 
HETATM 11 O O2' C2E . . . I 2 -55.196 4.657 39.305 1 51.52 ? O2' C2E 225 D 1 
HETATM 12 C C1' C2E . . . I 2 -53.101 3.811 38.468 1 47.78 ? C1' C2E 225 D 1 
HETATM 13 N N9 C2E . . . I 2 -52.406 2.514 38.475 1 49.68 ? N9 C2E 225 D 1 
HETATM 14 C C8 C2E . . . I 2 -51.064 2.296 38.659 1 45.7 ? C8 C2E 225 D 1 
HETATM 15 N N7 C2E . . . I 2 -50.772 1.061 38.373 1 43.36 ? N7 C2E 225 D 1 
HETATM 16 C C5 C2E . . . I 2 -51.923 0.382 38.134 1 45.87 ? C5 C2E 225 D 1 
HETATM 17 C C6 C2E . . . I 2 -52.225 -0.971 37.853 1 47.65 ? C6 C2E 225 D 1 
HETATM 18 O O6 C2E . . . I 2 -51.333 -1.794 37.742 1 50.51 ? O6 C2E 225 D 1 
HETATM 19 N N1 C2E . . . I 2 -53.521 -1.331 37.699 1 48.19 ? N1 C2E 225 D 1 
HETATM 20 C C2 C2E . . . I 2 -54.509 -0.394 37.812 1 52.72 ? C2 C2E 225 D 1 
HETATM 21 N N2 C2E . . . I 2 -55.815 -0.795 37.662 1 51 ? N2 C2E 225 D 1 
HETATM 22 N N3 C2E . . . I 2 -54.247 0.873 38.07 1 50.39 ? N3 C2E 225 D 1 
HETATM 23 C C4 C2E . . . I 2 -52.983 1.293 38.236 1 49.36 ? C4 C2E 225 D 1 
HETATM 24 P P11 C2E . . . I 2 -54.554 4.395 42.953 1 49.15 ? P11 C2E 225 D 1 
HETATM 25 O O21 C2E . . . I 2 -55.652 5.234 43.781 1 54.94 ? O21 C2E 225 D 1 
HETATM 26 O O11 C2E . . . I 2 -55.158 3.141 42.444 1 40.65 ? O11 C2E 225 D 1 
HETATM 27 O O5A C2E . . . I 2 -53.329 4.101 43.952 1 54.35 ? O5A C2E 225 D 1 
HETATM 28 C C5A C2E . . . I 2 -52.657 5.13 44.688 1 46.39 ? C5A C2E 225 D 1 
HETATM 29 C C4A C2E . . . I 2 -51.274 4.622 45.098 1 49.39 ? C4A C2E 225 D 1 
HETATM 30 O O4A C2E . . . I 2 -51.389 3.509 46.001 1 53.97 ? O4A C2E 225 D 1 
HETATM 31 C C3A C2E . . . I 2 -50.512 4.091 43.868 1 50.58 ? C3A C2E 225 D 1 
HETATM 32 O O3A C2E . . . I 2 -49.763 5.137 43.249 1 53.38 ? O3A C2E 225 D 1 
HETATM 33 C C2A C2E . . . I 2 -49.563 3.075 44.529 1 52.07 ? C2A C2E 225 D 1 
HETATM 34 O O2A C2E . . . I 2 -48.449 3.762 45.121 1 48.79 ? O2A C2E 225 D 1 
HETATM 35 C C1A C2E . . . I 2 -50.471 2.474 45.612 1 48.65 ? C1A C2E 225 D 1 
HETATM 36 N N91 C2E . . . I 2 -51.192 1.286 45.114 1 43.06 ? N91 C2E 225 D 1 
HETATM 37 C C81 C2E . . . I 2 -52.546 1.161 44.997 1 41.81 ? C81 C2E 225 D 1 
HETATM 38 N N71 C2E . . . I 2 -52.848 -0.095 44.873 1 46.39 ? N71 C2E 225 D 1 
HETATM 39 C C51 C2E . . . I 2 -51.72 -0.828 44.666 1 47.26 ? C51 C2E 225 D 1 
HETATM 40 C C61 C2E . . . I 2 -51.444 -2.205 44.368 1 51.09 ? C61 C2E 225 D 1 
HETATM 41 O O61 C2E . . . I 2 -52.327 -3.039 44.226 1 50.06 ? O61 C2E 225 D 1 
HETATM 42 N N11 C2E . . . I 2 -50.158 -2.594 44.243 1 49.92 ? N11 C2E 225 D 1 
HETATM 43 C C21 C2E . . . I 2 -49.169 -1.672 44.413 1 49.15 ? C21 C2E 225 D 1 
HETATM 44 N N21 C2E . . . I 2 -47.875 -2.104 44.3 1 52.94 ? N21 C2E 225 D 1 
HETATM 45 N N31 C2E . . . I 2 -49.401 -0.4 44.69 1 42.8 ? N31 C2E 225 D 1 
HETATM 46 C C41 C2E . . . I 2 -50.648 0.063 44.819 1 42.71 ? C41 C2E 225 D 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           46 
#