data_7LKQ
#
_model_server_result.job_id            042Xt-rS8QlW84qrrgpg_A 
_model_server_result.datetime_utc      '2025-03-04 15:10:58' 
_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          7lkq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":701}' 
#
_entry.id    7LKQ 
#
_exptl.entry_id    7LKQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              690.411 
_entity.id                          3 
_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    1 
_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            7LKQ 
_cell.length_a            96.1 
_cell.length_b            96.1 
_cell.length_c            146.334 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7LKQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        94 
_symmetry.space_group_name_Hall    'P 4n 2n' 
_symmetry.space_group_name_H-M     'P 42 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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_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,C,D,E,F,G,H,I 1 1 
B,G,H,I 2 1 
A,C,D,E,F 2 2 
#
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' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 96.1 96.1 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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                     7LKQ 
_atom_sites.fract_transf_matrix[1][1]    0.010406 
_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]    0.010406 
_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]    0.006834 
_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 3 C2E A 1 701 701 C2E C2E . 
D 4 SO4 A 1 702 5 SO4 SO4 . 
E 4 SO4 A 1 703 6 SO4 SO4 . 
F 5 MG A 1 704 1 MG MG . 
G 4 SO4 B 1 201 2 SO4 SO4 . 
H 4 SO4 B 1 202 3 SO4 SO4 . 
I 4 SO4 B 1 203 4 SO4 SO4 . 
#
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 3 31.801 50.874 21.375 1 55.97 ? P1 C2E 701 A 1 
HETATM 2 O O2P C2E . . . C 3 31.879 52.177 20.636 1 48.4 ? O2P C2E 701 A 1 
HETATM 3 O O1P C2E . . . C 3 32.435 49.699 20.69 1 74.82 ? O1P C2E 701 A 1 
HETATM 4 O O5' C2E . . . C 3 32.514 51.005 22.803 1 41.7 ? O5' C2E 701 A 1 
HETATM 5 C C5' C2E . . . C 3 33.905 50.619 22.788 1 35.76 ? C5' C2E 701 A 1 
HETATM 6 C C4' C2E . . . C 3 34.288 49.935 24.075 1 37.16 ? C4' C2E 701 A 1 
HETATM 7 O O4' C2E . . . C 3 35.732 49.922 24.177 1 42.97 ? O4' C2E 701 A 1 
HETATM 8 C C3' C2E . . . C 3 33.754 50.565 25.355 1 38.84 ? C3' C2E 701 A 1 
HETATM 9 O O3' C2E . . . C 3 33.267 49.548 26.215 1 47.26 ? O3' C2E 701 A 1 
HETATM 10 C C2' C2E . . . C 3 34.967 51.214 26.031 1 42.55 ? C2' C2E 701 A 1 
HETATM 11 O O2' C2E . . . C 3 35.055 50.878 27.397 1 38.4 ? O2' C2E 701 A 1 
HETATM 12 C C1' C2E . . . C 3 36.179 50.678 25.275 1 45.95 ? C1' C2E 701 A 1 
HETATM 13 N N9 C2E . . . C 3 37.111 51.697 24.803 1 56.42 ? N9 C2E 701 A 1 
HETATM 14 C C8 C2E . . . C 3 38.471 51.701 24.985 1 59.78 ? C8 C2E 701 A 1 
HETATM 15 N N7 C2E . . . C 3 39.066 52.738 24.447 1 65.62 ? N7 C2E 701 A 1 
HETATM 16 C C5 C2E . . . C 3 38.033 53.463 23.869 1 54 ? C5 C2E 701 A 1 
HETATM 17 C C6 C2E . . . C 3 38.064 54.677 23.143 1 47.1 ? C6 C2E 701 A 1 
HETATM 18 O O6 C2E . . . C 3 39.043 55.375 22.86 1 49.87 ? O6 C2E 701 A 1 
HETATM 19 N N1 C2E . . . C 3 36.791 55.065 22.735 1 53.05 ? N1 C2E 701 A 1 
HETATM 20 C C2 C2E . . . C 3 35.641 54.367 22.994 1 54.75 ? C2 C2E 701 A 1 
HETATM 21 N N2 C2E . . . C 3 34.496 54.876 22.533 1 62.75 ? N2 C2E 701 A 1 
HETATM 22 N N3 C2E . . . C 3 35.606 53.23 23.672 1 46.73 ? N3 C2E 701 A 1 
HETATM 23 C C4 C2E . . . C 3 36.83 52.833 24.082 1 55.92 ? C4 C2E 701 A 1 
HETATM 24 P P11 C2E . . . C 3 31.756 49.778 26.697 1 53.28 ? P11 C2E 701 A 1 
HETATM 25 O O21 C2E . . . C 3 31.23 48.444 27.126 1 64.7 ? O21 C2E 701 A 1 
HETATM 26 O O11 C2E . . . C 3 31.683 50.898 27.694 1 44.92 ? O11 C2E 701 A 1 
HETATM 27 O O5A C2E . . . C 3 30.996 50.191 25.35 1 45.16 ? O5A C2E 701 A 1 
HETATM 28 C C5A C2E . . . C 3 30.201 49.168 24.714 1 43.05 ? C5A C2E 701 A 1 
HETATM 29 C C4A C2E . . . C 3 29.228 49.807 23.757 1 47.33 ? C4A C2E 701 A 1 
HETATM 30 O O4A C2E . . . C 3 28.133 50.374 24.513 1 50.79 ? O4A C2E 701 A 1 
HETATM 31 C C3A C2E . . . C 3 29.776 50.968 22.946 1 54.92 ? C3A C2E 701 A 1 
HETATM 32 O O3A C2E . . . C 3 30.274 50.505 21.7 1 45.76 ? O3A C2E 701 A 1 
HETATM 33 C C2A C2E . . . C 3 28.505 51.752 22.63 1 61.68 ? C2A C2E 701 A 1 
HETATM 34 O O2A C2E . . . C 3 27.88 51.266 21.464 1 69.97 ? O2A C2E 701 A 1 
HETATM 35 C C1A C2E . . . C 3 27.624 51.506 23.852 1 50.68 ? C1A C2E 701 A 1 
HETATM 36 N N91 C2E . . . C 3 27.6 52.614 24.796 1 49.63 ? N91 C2E 701 A 1 
HETATM 37 C C81 C2E . . . C 3 28.573 52.931 25.706 1 46.76 ? C81 C2E 701 A 1 
HETATM 38 N N71 C2E . . . C 3 28.282 53.982 26.428 1 44.12 ? N71 C2E 701 A 1 
HETATM 39 C C51 C2E . . . C 3 27.038 54.381 25.965 1 46.82 ? C51 C2E 701 A 1 
HETATM 40 C C61 C2E . . . C 3 26.225 55.462 26.375 1 62.02 ? C61 C2E 701 A 1 
HETATM 41 O O61 C2E . . . C 3 26.456 56.304 27.253 1 67.83 ? O61 C2E 701 A 1 
HETATM 42 N N11 C2E . . . C 3 25.038 55.509 25.647 1 57.11 ? N11 C2E 701 A 1 
HETATM 43 C C21 C2E . . . C 3 24.684 54.631 24.655 1 58.69 ? C21 C2E 701 A 1 
HETATM 44 N N21 C2E . . . C 3 23.5 54.841 24.067 1 75.74 ? N21 C2E 701 A 1 
HETATM 45 N N31 C2E . . . C 3 25.446 53.61 24.265 1 41.94 ? N31 C2E 701 A 1 
HETATM 46 C C41 C2E . . . C 3 26.605 53.547 24.961 1 44.8 ? C41 C2E 701 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           46 
#