data_6PFV
#
_model_server_result.job_id            qwKYXMq2zVyadnvcKYlYbg 
_model_server_result.datetime_utc      '2024-10-15 14:29:59' 
_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          6pfv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":201}' 
#
_entry.id    6PFV 
#
_exptl.entry_id    6PFV 
_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    6 
_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            6PFV 
_cell.length_a            79.847 
_cell.length_b            97.339 
_cell.length_c            204.58 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
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 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,G,H 1 1 
C,D,I,J 2 1 
E,F,K,L 3 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
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L 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                     6PFV 
_atom_sites.fract_transf_matrix[1][1]    0.012524 
_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]    0.010273 
_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]    0.004888 
_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
G 3 C2E T 1 201 203 C2E C2E . 
H 3 C2E T 1 202 201 C2E C2E . 
I 3 C2E B 1 201 203 C2E C2E . 
J 3 C2E B 1 202 201 C2E C2E . 
K 3 C2E E 1 201 203 C2E C2E . 
L 3 C2E E 1 202 201 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 . . . K 3 88.787 30.683 2.341 1 164.65 ? P1 C2E 201 E 1 
HETATM 2 O O2P C2E . . . K 3 89.268 32.093 2.374 1 81.82 ? O2P C2E 201 E 1 
HETATM 3 O O1P C2E . . . K 3 87.666 30.097 1.545 1 93.66 ? O1P C2E 201 E 1 
HETATM 4 O O5' C2E . . . K 3 88.474 30.236 3.918 1 89.22 ? O5' C2E 201 E 1 
HETATM 5 C C5' C2E . . . K 3 88.48 28.948 4.103 1 82.19 ? C5' C2E 201 E 1 
HETATM 6 C C4' C2E . . . K 3 88.324 28.505 5.53 1 90.15 ? C4' C2E 201 E 1 
HETATM 7 O O4' C2E . . . K 3 87.177 29.182 6.141 1 93.12 ? O4' C2E 201 E 1 
HETATM 8 C C3' C2E . . . K 3 87.968 27.018 5.405 1 118.65 ? C3' C2E 201 E 1 
HETATM 9 O O3' C2E . . . K 3 88.856 26.141 5.992 1 144.5 ? O3' C2E 201 E 1 
HETATM 10 C C2' C2E . . . K 3 86.408 26.812 5.814 1 100 ? C2' C2E 201 E 1 
HETATM 11 O O2' C2E . . . K 3 86.229 25.834 6.867 1 98.16 ? O2' C2E 201 E 1 
HETATM 12 C C1' C2E . . . K 3 86.014 28.308 6.283 1 96.65 ? C1' C2E 201 E 1 
HETATM 13 N N9 C2E . . . K 3 85.09 28.608 5.286 1 110.42 ? N9 C2E 201 E 1 
HETATM 14 C C8 C2E . . . K 3 85.327 28.36 3.943 1 107.05 ? C8 C2E 201 E 1 
HETATM 15 N N7 C2E . . . K 3 84.28 28.598 3.178 1 104.11 ? N7 C2E 201 E 1 
HETATM 16 C C5 C2E . . . K 3 83.284 28.978 4.048 1 116.28 ? C5 C2E 201 E 1 
HETATM 17 C C6 C2E . . . K 3 81.955 29.346 3.716 1 120.06 ? C6 C2E 201 E 1 
HETATM 18 O O6 C2E . . . K 3 81.362 29.429 2.643 1 107.47 ? O6 C2E 201 E 1 
HETATM 19 N N1 C2E . . . K 3 81.204 29.682 4.881 1 119.5 ? N1 C2E 201 E 1 
HETATM 20 C C2 C2E . . . K 3 81.752 29.645 6.183 1 119.08 ? C2 C2E 201 E 1 
HETATM 21 N N2 C2E . . . K 3 80.9 30 7.212 1 129.2 ? N2 C2E 201 E 1 
HETATM 22 N N3 C2E . . . K 3 83.026 29.299 6.53 1 134.65 ? N3 C2E 201 E 1 
HETATM 23 C C4 C2E . . . K 3 83.749 28.969 5.39 1 125.81 ? C4 C2E 201 E 1 
HETATM 24 P P11 C2E . . . K 3 89.758 25.179 4.898 1 139.3 ? P11 C2E 201 E 1 
HETATM 25 O O21 C2E . . . K 3 91.094 24.885 5.5 1 64.44 ? O21 C2E 201 E 1 
HETATM 26 O O11 C2E . . . K 3 88.784 24.207 4.323 1 133.43 ? O11 C2E 201 E 1 
HETATM 27 O O5A C2E . . . K 3 89.973 26.32 3.665 1 102.99 ? O5A C2E 201 E 1 
HETATM 28 C C5A C2E . . . K 3 91.12 27.101 3.617 1 97.1 ? C5A C2E 201 E 1 
HETATM 29 C C4A C2E . . . K 3 91.339 27.657 2.155 1 101.26 ? C4A C2E 201 E 1 
HETATM 30 O O4A C2E . . . K 3 91.617 26.56 1.274 1 104.77 ? O4A C2E 201 E 1 
HETATM 31 C C3A C2E . . . K 3 90.105 28.396 1.614 1 113.12 ? C3A C2E 201 E 1 
HETATM 32 O O3A C2E . . . K 3 90.161 29.719 2.019 1 115.66 ? O3A C2E 201 E 1 
HETATM 33 C C2A C2E . . . K 3 90.346 28.238 0.088 1 100.23 ? C2A C2E 201 E 1 
HETATM 34 O O2A C2E . . . K 3 91.151 29.255 -0.327 1 64.58 ? O2A C2E 201 E 1 
HETATM 35 C C1A C2E . . . K 3 91.136 26.891 0.006 1 98.3 ? C1A C2E 201 E 1 
HETATM 36 N N91 C2E . . . K 3 90.211 25.818 -0.344 1 100.07 ? N91 C2E 201 E 1 
HETATM 37 C C81 C2E . . . K 3 89.73 24.805 0.493 1 80.7 ? C81 C2E 201 E 1 
HETATM 38 N N71 C2E . . . K 3 88.891 23.997 -0.154 1 69.17 ? N71 C2E 201 E 1 
HETATM 39 C C51 C2E . . . K 3 88.805 24.478 -1.424 1 73.62 ? C51 C2E 201 E 1 
HETATM 40 C C61 C2E . . . K 3 88.033 23.952 -2.484 1 61.64 ? C61 C2E 201 E 1 
HETATM 41 O O61 C2E . . . K 3 87.282 22.99 -2.543 1 67.38 ? O61 C2E 201 E 1 
HETATM 42 N N11 C2E . . . K 3 88.193 24.714 -3.67 1 64.1 ? N11 C2E 201 E 1 
HETATM 43 C C21 C2E . . . K 3 89.028 25.849 -3.74 1 74.59 ? C21 C2E 201 E 1 
HETATM 44 N N21 C2E . . . K 3 89.087 26.491 -4.953 1 80.42 ? N21 C2E 201 E 1 
HETATM 45 N N31 C2E . . . K 3 89.776 26.366 -2.729 1 66.12 ? N31 C2E 201 E 1 
HETATM 46 C C41 C2E . . . K 3 89.617 25.621 -1.58 1 85.93 ? C41 C2E 201 E 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           46 
#