data_6PFV
#
_model_server_result.job_id            c2W6zOv4p9NJ7OMx8eHqoQ 
_model_server_result.datetime_utc      '2024-10-15 14:22:37' 
_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":"H","auth_seq_id":202}' 
#
_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 . . . H 3 34.525 26.853 19.649 1 42.28 ? P1 C2E 202 T 1 
HETATM 2 O O2P C2E . . . H 3 34.849 25.53 19.045 1 107.1 ? O2P C2E 202 T 1 
HETATM 3 O O1P C2E . . . H 3 35.216 28.158 19.428 1 95.72 ? O1P C2E 202 T 1 
HETATM 4 O O5' C2E . . . H 3 34.486 26.651 21.299 1 53 ? O5' C2E 202 T 1 
HETATM 5 C C5' C2E . . . H 3 34.562 27.739 22.021 1 46.53 ? C5' C2E 202 T 1 
HETATM 6 C C4' C2E . . . H 3 34.055 27.502 23.424 1 54.04 ? C4' C2E 202 T 1 
HETATM 7 O O4' C2E . . . H 3 35.219 27.189 24.273 1 60.41 ? O4' C2E 202 T 1 
HETATM 8 C C3' C2E . . . H 3 33.445 28.844 23.913 1 60.61 ? C3' C2E 202 T 1 
HETATM 9 O O3' C2E . . . H 3 32.21 28.717 24.52 1 57.75 ? O3' C2E 202 T 1 
HETATM 10 C C2' C2E . . . H 3 34.574 29.559 24.834 1 57.1 ? C2' C2E 202 T 1 
HETATM 11 O O2' C2E . . . H 3 34.068 29.965 26.108 1 72.55 ? O2' C2E 202 T 1 
HETATM 12 C C1' C2E . . . H 3 35.704 28.379 24.95 1 62.81 ? C1' C2E 202 T 1 
HETATM 13 N N9 C2E . . . H 3 36.75 28.952 24.232 1 86.28 ? N9 C2E 202 T 1 
HETATM 14 C C8 C2E . . . H 3 36.552 29.661 23.073 1 62.09 ? C8 C2E 202 T 1 
HETATM 15 N N7 C2E . . . H 3 37.638 30.21 22.591 1 61.42 ? N7 C2E 202 T 1 
HETATM 16 C C5 C2E . . . H 3 38.615 29.886 23.498 1 77.88 ? C5 C2E 202 T 1 
HETATM 17 C C6 C2E . . . H 3 39.979 30.249 23.434 1 68.13 ? C6 C2E 202 T 1 
HETATM 18 O O6 C2E . . . H 3 40.619 30.917 22.631 1 68.55 ? O6 C2E 202 T 1 
HETATM 19 N N1 C2E . . . H 3 40.697 29.739 24.56 1 75.39 ? N1 C2E 202 T 1 
HETATM 20 C C2 C2E . . . H 3 40.085 28.974 25.58 1 83.6 ? C2 C2E 202 T 1 
HETATM 21 N N2 C2E . . . H 3 40.908 28.547 26.604 1 87.02 ? N2 C2E 202 T 1 
HETATM 22 N N3 C2E . . . H 3 38.772 28.609 25.661 1 99.7 ? N3 C2E 202 T 1 
HETATM 23 C C4 C2E . . . H 3 38.087 29.116 24.566 1 89.65 ? C4 C2E 202 T 1 
HETATM 24 P P11 C2E . . . H 3 30.918 29.559 23.764 1 55.98 ? P11 C2E 202 T 1 
HETATM 25 O O21 C2E . . . H 3 29.631 28.87 24.073 1 108.84 ? O21 C2E 202 T 1 
HETATM 26 O O11 C2E . . . H 3 31.242 31.008 23.889 1 64.3 ? O11 C2E 202 T 1 
HETATM 27 O O5A C2E . . . H 3 31.302 29.232 22.165 1 51.74 ? O5A C2E 202 T 1 
HETATM 28 C C5A C2E . . . H 3 30.896 28.035 21.598 1 60.85 ? C5A C2E 202 T 1 
HETATM 29 C C4A C2E . . . H 3 30.897 28.165 20.031 1 57.48 ? C4A C2E 202 T 1 
HETATM 30 O O4A C2E . . . H 3 30.158 29.325 19.644 1 67.28 ? O4A C2E 202 T 1 
HETATM 31 C C3A C2E . . . H 3 32.321 28.333 19.502 1 67.43 ? C3A C2E 202 T 1 
HETATM 32 O O3A C2E . . . H 3 32.892 27.113 19.349 1 81.03 ? O3A C2E 202 T 1 
HETATM 33 C C2A C2E . . . H 3 32.028 28.983 18.146 1 61.19 ? C2A C2E 202 T 1 
HETATM 34 O O2A C2E . . . H 3 31.76 28.007 17.228 1 92.45 ? O2A C2E 202 T 1 
HETATM 35 C C1A C2E . . . H 3 30.716 29.796 18.463 1 52.94 ? C1A C2E 202 T 1 
HETATM 36 N N91 C2E . . . H 3 31.094 31.165 18.751 1 63.74 ? N91 C2E 202 T 1 
HETATM 37 C C81 C2E . . . H 3 31.288 31.769 20.009 1 56.52 ? C81 C2E 202 T 1 
HETATM 38 N N71 C2E . . . H 3 31.658 33.052 19.892 1 67.37 ? N71 C2E 202 T 1 
HETATM 39 C C51 C2E . . . H 3 31.713 33.282 18.528 1 70.68 ? C51 C2E 202 T 1 
HETATM 40 C C61 C2E . . . H 3 32.055 34.485 17.871 1 69.46 ? C61 C2E 202 T 1 
HETATM 41 O O61 C2E . . . H 3 32.371 35.58 18.308 1 50.96 ? O61 C2E 202 T 1 
HETATM 42 N N11 C2E . . . H 3 32.006 34.352 16.454 1 52.85 ? N11 C2E 202 T 1 
HETATM 43 C C21 C2E . . . H 3 31.654 33.154 15.814 1 54.42 ? C21 C2E 202 T 1 
HETATM 44 N N21 C2E . . . H 3 31.646 33.166 14.429 1 73.29 ? N21 C2E 202 T 1 
HETATM 45 N N31 C2E . . . H 3 31.324 31.989 16.427 1 54.58 ? N31 C2E 202 T 1 
HETATM 46 C C41 C2E . . . H 3 31.373 32.122 17.802 1 49.21 ? C41 C2E 202 T 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           192 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           46 
#