data_1W25
#
_model_server_result.job_id            XHsXtAJFBRc1z_5eoXcOKQ 
_model_server_result.datetime_utc      '2024-11-28 23:05:43' 
_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          1w25 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":503}' 
#
_entry.id    1W25 
#
_exptl.entry_id    1W25 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              690.411 
_entity.id                          4 
_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    5 
_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            1W25 
_cell.length_a            135.87 
_cell.length_b            135.87 
_cell.length_c            169.247 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1W25 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        94 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 42 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 4 E N N 
? 4 F N N 
? 4 G N N 
? 4 I N N 
? 4 J N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A OD1 ASP 8 A ASP 9 1_555 D MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? 
metalc ? metalc2 A OD1 ASP 9 A ASP 10 1_555 D MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc3 A OD2 ASP 52 A ASP 53 1_555 D MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? 
metalc ? metalc4 A O MET 54 A MET 55 1_555 D MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc5 B OD1 ASP 8 B ASP 9 1_555 H MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc6 B OD1 ASP 9 B ASP 10 1_555 H MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? 
metalc ? metalc7 B OD2 ASP 52 B ASP 53 1_555 H MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? 
metalc ? metalc8 B O MET 54 B MET 55 1_555 H MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
#
_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                     1W25 
_atom_sites.fract_transf_matrix[1][1]    0.00736 
_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]    0.00736 
_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]    0.005909 
_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 2 ZN A 1 499 499 ZN ZN . 
D 3 MG A 1 500 500 MG MG . 
E 4 C2E A 1 501 501 C2E C2E . 
F 4 C2E A 1 503 503 C2E C2E . 
G 4 C2E A 1 505 505 C2E C2E . 
H 3 MG B 1 500 500 MG MG . 
I 4 C2E B 1 503 503 C2E C2E . 
J 4 C2E B 1 505 505 C2E C2E . 
K 5 HOH A 1 2001 2001 HOH HOH . 
K 5 HOH A 2 2002 2002 HOH HOH . 
K 5 HOH A 3 2003 2003 HOH HOH . 
K 5 HOH A 4 2004 2004 HOH HOH . 
K 5 HOH A 5 2005 2005 HOH HOH . 
K 5 HOH A 6 2006 2006 HOH HOH . 
K 5 HOH A 7 2007 2007 HOH HOH . 
L 5 HOH B 1 2001 2001 HOH HOH . 
L 5 HOH B 2 2002 2002 HOH HOH . 
L 5 HOH B 3 2003 2003 HOH HOH . 
L 5 HOH B 4 2004 2004 HOH HOH . 
L 5 HOH B 5 2005 2005 HOH HOH . 
L 5 HOH B 6 2006 2006 HOH HOH . 
L 5 HOH B 7 2007 2007 HOH HOH . 
L 5 HOH B 8 2008 2008 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 4 95.505 -4.7 58.928 1 23.22 ? P1 C2E 503 A 1 
HETATM 2 O O2P C2E . . . F 4 95.656 -3.217 58.927 1 26.89 ? O2P C2E 503 A 1 
HETATM 3 O O1P C2E . . . F 4 95.253 -5.195 57.529 1 27.82 ? O1P C2E 503 A 1 
HETATM 4 O O5' C2E . . . F 4 96.835 -5.415 59.464 1 25.51 ? O5' C2E 503 A 1 
HETATM 5 C C5' C2E . . . F 4 96.838 -6.836 59.452 1 25.6 ? C5' C2E 503 A 1 
HETATM 6 C C4' C2E . . . F 4 98.019 -7.393 60.232 1 25.1 ? C4' C2E 503 A 1 
HETATM 7 O O4' C2E . . . F 4 99.24 -6.85 59.724 1 25.66 ? O4' C2E 503 A 1 
HETATM 8 C C3' C2E . . . F 4 98.009 -7.094 61.725 1 22.74 ? C3' C2E 503 A 1 
HETATM 9 O O3' C2E . . . F 4 97.23 -8.073 62.407 1 22.93 ? O3' C2E 503 A 1 
HETATM 10 C C2' C2E . . . F 4 99.491 -7.159 62.048 1 24.36 ? C2' C2E 503 A 1 
HETATM 11 O O2' C2E . . . F 4 99.938 -8.501 62.294 1 24.56 ? O2' C2E 503 A 1 
HETATM 12 C C1' C2E . . . F 4 100.171 -6.657 60.789 1 23.97 ? C1' C2E 503 A 1 
HETATM 13 N N9 C2E . . . F 4 100.514 -5.218 60.852 1 24.4 ? N9 C2E 503 A 1 
HETATM 14 C C8 C2E . . . F 4 99.982 -4.253 60.077 1 24.12 ? C8 C2E 503 A 1 
HETATM 15 N N7 C2E . . . F 4 100.527 -3.055 60.379 1 22.11 ? N7 C2E 503 A 1 
HETATM 16 C C5 C2E . . . F 4 101.417 -3.235 61.362 1 22.56 ? C5 C2E 503 A 1 
HETATM 17 C C6 C2E . . . F 4 102.339 -2.385 62.14 1 23.36 ? C6 C2E 503 A 1 
HETATM 18 O O6 C2E . . . F 4 102.43 -1.156 61.961 1 24.78 ? O6 C2E 503 A 1 
HETATM 19 N N1 C2E . . . F 4 103.097 -2.963 63.064 1 24.35 ? N1 C2E 503 A 1 
HETATM 20 C C2 C2E . . . F 4 103.049 -4.277 63.305 1 23.45 ? C2 C2E 503 A 1 
HETATM 21 N N2 C2E . . . F 4 103.848 -4.785 64.265 1 23.6 ? N2 C2E 503 A 1 
HETATM 22 N N3 C2E . . . F 4 102.229 -5.121 62.63 1 24.32 ? N3 C2E 503 A 1 
HETATM 23 C C4 C2E . . . F 4 101.408 -4.666 61.666 1 23.2 ? C4 C2E 503 A 1 
HETATM 24 P P11 C2E . . . F 4 96.633 -7.451 63.737 1 23.09 ? P11 C2E 503 A 1 
HETATM 25 O O21 C2E . . . F 4 97.754 -6.887 64.569 1 20.03 ? O21 C2E 503 A 1 
HETATM 26 O O11 C2E . . . F 4 95.909 -8.537 64.506 1 22.92 ? O11 C2E 503 A 1 
HETATM 27 O O5A C2E . . . F 4 95.543 -6.339 63.354 1 23.3 ? O5A C2E 503 A 1 
HETATM 28 C C5A C2E . . . F 4 94.366 -6.735 62.669 1 24.34 ? C5A C2E 503 A 1 
HETATM 29 C C4A C2E . . . F 4 93.638 -5.503 62.158 1 26.03 ? C4A C2E 503 A 1 
HETATM 30 O O4A C2E . . . F 4 93.265 -4.665 63.255 1 25.66 ? O4A C2E 503 A 1 
HETATM 31 C C3A C2E . . . F 4 94.463 -4.647 61.197 1 25.65 ? C3A C2E 503 A 1 
HETATM 32 O O3A C2E . . . F 4 94.261 -5.112 59.852 1 26.7 ? O3A C2E 503 A 1 
HETATM 33 C C2A C2E . . . F 4 93.87 -3.286 61.437 1 24.34 ? C2A C2E 503 A 1 
HETATM 34 O O2A C2E . . . F 4 92.723 -3.112 60.612 1 23.55 ? O2A C2E 503 A 1 
HETATM 35 C C1A C2E . . . F 4 93.444 -3.304 62.888 1 24.17 ? C1A C2E 503 A 1 
HETATM 36 N N91 C2E . . . F 4 94.468 -2.676 63.754 1 24.45 ? N91 C2E 503 A 1 
HETATM 37 C C81 C2E . . . F 4 95.38 -3.273 64.55 1 24.2 ? C81 C2E 503 A 1 
HETATM 38 N N71 C2E . . . F 4 96.123 -2.338 65.198 1 23.82 ? N71 C2E 503 A 1 
HETATM 39 C C51 C2E . . . F 4 95.682 -1.123 64.812 1 23.12 ? C51 C2E 503 A 1 
HETATM 40 C C61 C2E . . . F 4 96 0.287 65.102 1 24 ? C61 C2E 503 A 1 
HETATM 41 O O61 C2E . . . F 4 96.909 0.598 65.895 1 23.59 ? O61 C2E 503 A 1 
HETATM 42 N N11 C2E . . . F 4 95.291 1.234 64.476 1 25 ? N11 C2E 503 A 1 
HETATM 43 C C21 C2E . . . F 4 94.308 0.945 63.61 1 24.24 ? C21 C2E 503 A 1 
HETATM 44 N N21 C2E . . . F 4 93.639 1.959 63.025 1 25.28 ? N21 C2E 503 A 1 
HETATM 45 N N31 C2E . . . F 4 93.953 -0.319 63.298 1 22.58 ? N31 C2E 503 A 1 
HETATM 46 C C41 C2E . . . F 4 94.594 -1.359 63.863 1 23.31 ? C41 C2E 503 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           465 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           46 
#