data_3KLO
#
_model_server_result.job_id            vld3MljDRMiVWRN9yPYBnw 
_model_server_result.datetime_utc      '2024-12-20 06:15:08' 
_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":"F","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 . . . F 2 -55.651 11.745 2.102 1 25.14 ? P1 C2E 225 B 1 
HETATM 2 O O2P C2E . . . F 2 -54.287 12.597 2.231 1 27.21 ? O2P C2E 225 B 1 
HETATM 3 O O1P C2E . . . F 2 -56.859 12.567 2.237 1 22.68 ? O1P C2E 225 B 1 
HETATM 4 O O5' C2E . . . F 2 -55.606 10.593 3.199 1 28.3 ? O5' C2E 225 B 1 
HETATM 5 C C5' C2E . . . F 2 -54.582 9.597 3.169 1 25.47 ? C5' C2E 225 B 1 
HETATM 6 C C4' C2E . . . F 2 -55.075 8.354 3.913 1 27.2 ? C4' C2E 225 B 1 
HETATM 7 O O4' C2E . . . F 2 -55.768 8.683 5.132 1 23.55 ? O4' C2E 225 B 1 
HETATM 8 C C3' C2E . . . F 2 -56.107 7.602 3.064 1 25.08 ? C3' C2E 225 B 1 
HETATM 9 O O3' C2E . . . F 2 -55.515 6.789 2.073 1 22.39 ? O3' C2E 225 B 1 
HETATM 10 C C2' C2E . . . F 2 -56.791 6.755 4.135 1 27.46 ? C2' C2E 225 B 1 
HETATM 11 O O2' C2E . . . F 2 -55.915 5.658 4.421 1 27.37 ? O2' C2E 225 B 1 
HETATM 12 C C1' C2E . . . F 2 -56.797 7.709 5.339 1 25.01 ? C1' C2E 225 B 1 
HETATM 13 N N9 C2E . . . F 2 -58.075 8.407 5.345 1 26.38 ? N9 C2E 225 B 1 
HETATM 14 C C8 C2E . . . F 2 -58.27 9.741 5.137 1 25.08 ? C8 C2E 225 B 1 
HETATM 15 N N7 C2E . . . F 2 -59.517 10.04 5.367 1 26.75 ? N7 C2E 225 B 1 
HETATM 16 C C5 C2E . . . F 2 -60.203 8.906 5.646 1 26.49 ? C5 C2E 225 B 1 
HETATM 17 C C6 C2E . . . F 2 -61.553 8.615 5.93 1 29.29 ? C6 C2E 225 B 1 
HETATM 18 O O6 C2E . . . F 2 -62.376 9.507 6.008 1 33.29 ? O6 C2E 225 B 1 
HETATM 19 N N1 C2E . . . F 2 -61.927 7.335 6.127 1 30.95 ? N1 C2E 225 B 1 
HETATM 20 C C2 C2E . . . F 2 -60.992 6.348 6.054 1 33.79 ? C2 C2E 225 B 1 
HETATM 21 N N2 C2E . . . F 2 -61.391 5.045 6.225 1 32.44 ? N2 C2E 225 B 1 
HETATM 22 N N3 C2E . . . F 2 -59.724 6.604 5.796 1 32.17 ? N3 C2E 225 B 1 
HETATM 23 C C4 C2E . . . F 2 -59.297 7.849 5.585 1 28.32 ? C4 C2E 225 B 1 
HETATM 24 P P11 C2E . . . F 2 -56.376 6.265 0.82 1 28.2 ? P11 C2E 225 B 1 
HETATM 25 O O21 C2E . . . F 2 -55.497 5.235 -0.053 1 28.05 ? O21 C2E 225 B 1 
HETATM 26 O O11 C2E . . . F 2 -57.643 5.651 1.29 1 24.25 ? O11 C2E 225 B 1 
HETATM 27 O O5A C2E . . . F 2 -56.661 7.503 -0.148 1 28.5 ? O5A C2E 225 B 1 
HETATM 28 C C5A C2E . . . F 2 -55.584 8.254 -0.703 1 22.98 ? C5A C2E 225 B 1 
HETATM 29 C C4A C2E . . . F 2 -56.13 9.615 -1.099 1 25.5 ? C4A C2E 225 B 1 
HETATM 30 O O4A C2E . . . F 2 -57.188 9.507 -2.054 1 26.1 ? O4A C2E 225 B 1 
HETATM 31 C C3A C2E . . . F 2 -56.718 10.299 0.133 1 25.33 ? C3A C2E 225 B 1 
HETATM 32 O O3A C2E . . . F 2 -55.635 11.023 0.68 1 25.75 ? O3A C2E 225 B 1 
HETATM 33 C C2A C2E . . . F 2 -57.702 11.263 -0.54 1 26.45 ? C2A C2E 225 B 1 
HETATM 34 O O2A C2E . . . F 2 -56.984 12.372 -1.087 1 26.85 ? O2A C2E 225 B 1 
HETATM 35 C C1A C2E . . . F 2 -58.22 10.418 -1.701 1 23.68 ? C1A C2E 225 B 1 
HETATM 36 N N91 C2E . . . F 2 -59.404 9.685 -1.264 1 25.07 ? N91 C2E 225 B 1 
HETATM 37 C C81 C2E . . . F 2 -59.532 8.344 -1.057 1 27.38 ? C81 C2E 225 B 1 
HETATM 38 N N71 C2E . . . F 2 -60.788 8.046 -0.9 1 28.56 ? N71 C2E 225 B 1 
HETATM 39 C C51 C2E . . . F 2 -61.483 9.196 -0.738 1 27.08 ? C51 C2E 225 B 1 
HETATM 40 C C61 C2E . . . F 2 -62.815 9.521 -0.401 1 30.06 ? C61 C2E 225 B 1 
HETATM 41 O O61 C2E . . . F 2 -63.65 8.679 -0.153 1 35.14 ? O61 C2E 225 B 1 
HETATM 42 N N11 C2E . . . F 2 -63.164 10.809 -0.322 1 29.38 ? N11 C2E 225 B 1 
HETATM 43 C C21 C2E . . . F 2 -62.263 11.782 -0.571 1 29.57 ? C21 C2E 225 B 1 
HETATM 44 N N21 C2E . . . F 2 -62.688 13.081 -0.464 1 35.23 ? N21 C2E 225 B 1 
HETATM 45 N N31 C2E . . . F 2 -61.017 11.515 -0.887 1 26.33 ? N31 C2E 225 B 1 
HETATM 46 C C41 C2E . . . F 2 -60.6 10.251 -0.972 1 26.31 ? C41 C2E 225 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           46 
#