data_6ZXM
#
_model_server_result.job_id            qyG87faoZQ2gTdS_NA5oTg 
_model_server_result.datetime_utc      '2024-12-01 07:11:51' 
_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          6zxm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":302}' 
#
_entry.id    6ZXM 
#
_exptl.entry_id    6ZXM 
_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    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          118.2 
_cell.angle_gamma         90 
_cell.entry_id            6ZXM 
_cell.length_a            122.603 
_cell.length_b            72.917 
_cell.length_c            125.729 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6ZXM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 
? dimeric 2 author_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,I,J,K,L 1 1 
C,D,M,N,O,P,Q,R 2 1 
E,F,S,T,U,V,W,X 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
? 2 G N N 
? 2 H N N 
? 2 J N N 
? 2 K N N 
? 2 M N N 
? 2 N N N 
? 2 P N N 
? 2 Q N N 
? 2 S N N 
? 2 T N N 
? 2 V N N 
? 2 W 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 OE2 GLU 32 A GLU 12 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc2 A OD1 ASP 33 A ASP 13 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc3 A OD2 ASP 76 A ASP 56 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc4 B OE2 GLU 32 B GLU 12 1_555 L MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc5 B OD1 ASP 33 B ASP 13 1_555 L MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc6 B OD2 ASP 76 B ASP 56 1_555 L MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc7 L MG MG . B MG 303 1_555 F O GLY 107 F GLY 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? 
metalc ? metalc8 C OE2 GLU 32 C GLU 12 1_555 O MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc9 C OD1 ASP 33 C ASP 13 1_555 O MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc10 C OD2 ASP 76 C ASP 56 1_555 O MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc11 D OE2 GLU 32 D GLU 12 1_555 R MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc12 D OD1 ASP 33 D ASP 13 1_555 R MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc13 D OD2 ASP 76 D ASP 56 1_555 R MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc14 E OE2 GLU 32 E GLU 12 1_555 U MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc15 E OD1 ASP 33 E ASP 13 1_555 U MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc16 E OD2 ASP 76 E ASP 56 1_555 U MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc17 F OE2 GLU 32 F GLU 12 1_555 X MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc18 F OD1 ASP 33 F ASP 13 1_555 X MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc19 F OD2 ASP 76 F ASP 56 1_555 X MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
#
_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                     6ZXM 
_atom_sites.fract_transf_matrix[1][1]    0.008156 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004374 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013714 
_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]    0.009025 
_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 2 C2E A 1 301 301 C2E C2E . 
H 2 C2E A 1 302 302 C2E C2E . 
I 3 MG A 1 303 303 MG MG . 
J 2 C2E B 1 301 301 C2E C2E . 
K 2 C2E B 1 302 302 C2E C2E . 
L 3 MG B 1 303 303 MG MG . 
M 2 C2E C 1 301 301 C2E C2E . 
N 2 C2E C 1 302 302 C2E C2E . 
O 3 MG C 1 303 303 MG MG . 
P 2 C2E D 1 301 301 C2E C2E . 
Q 2 C2E D 1 302 302 C2E C2E . 
R 3 MG D 1 303 303 MG MG . 
S 2 C2E E 1 301 301 C2E C2E . 
T 2 C2E E 1 302 302 C2E C2E . 
U 3 MG E 1 303 303 MG MG . 
V 2 C2E F 1 301 301 C2E C2E . 
W 2 C2E F 1 302 302 C2E C2E . 
X 3 MG F 1 303 303 MG MG . 
#
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 2 -28.994 -15.92 -91.004 1 92.38 ? P1 C2E 302 A 1 
HETATM 2 O O2P C2E . . . H 2 -29.236 -15.951 -92.49 1 92.97 ? O2P C2E 302 A 1 
HETATM 3 O O1P C2E . . . H 2 -29.249 -17.229 -90.307 1 94.88 ? O1P C2E 302 A 1 
HETATM 4 O O5' C2E . . . H 2 -27.454 -15.475 -90.842 1 93.71 ? O5' C2E 302 A 1 
HETATM 5 C C5' C2E . . . H 2 -27.011 -15.149 -89.497 1 93.07 ? C5' C2E 302 A 1 
HETATM 6 C C4' C2E . . . H 2 -25.769 -14.297 -89.557 1 89.92 ? C4' C2E 302 A 1 
HETATM 7 O O4' C2E . . . H 2 -24.888 -14.843 -90.562 1 89.58 ? O4' C2E 302 A 1 
HETATM 8 C C3' C2E . . . H 2 -26.01 -12.836 -89.935 1 86.34 ? C3' C2E 302 A 1 
HETATM 9 O O3' C2E . . . H 2 -26.193 -12.007 -88.782 1 84.65 ? O3' C2E 302 A 1 
HETATM 10 C C2' C2E . . . H 2 -24.727 -12.455 -90.656 1 85.4 ? C2' C2E 302 A 1 
HETATM 11 O O2' C2E . . . H 2 -23.775 -11.839 -89.823 1 79.7 ? O2' C2E 302 A 1 
HETATM 12 C C1' C2E . . . H 2 -24.294 -13.785 -91.266 1 90.72 ? C1' C2E 302 A 1 
HETATM 13 N N9 C2E . . . H 2 -24.769 -13.874 -92.625 1 98.43 ? N9 C2E 302 A 1 
HETATM 14 C C8 C2E . . . H 2 -25.733 -14.71 -93.128 1 105.02 ? C8 C2E 302 A 1 
HETATM 15 N N7 C2E . . . H 2 -25.959 -14.51 -94.406 1 111.38 ? N7 C2E 302 A 1 
HETATM 16 C C5 C2E . . . H 2 -25.119 -13.444 -94.746 1 109.45 ? C5 C2E 302 A 1 
HETATM 17 C C6 C2E . . . H 2 -24.93 -12.772 -95.988 1 108.63 ? C6 C2E 302 A 1 
HETATM 18 O O6 C2E . . . H 2 -25.495 -12.997 -97.073 1 110.81 ? O6 C2E 302 A 1 
HETATM 19 N N1 C2E . . . H 2 -23.984 -11.741 -95.877 1 105.4 ? N1 C2E 302 A 1 
HETATM 20 C C2 C2E . . . H 2 -23.292 -11.416 -94.727 1 101.17 ? C2 C2E 302 A 1 
HETATM 21 N N2 C2E . . . H 2 -22.418 -10.402 -94.804 1 96.71 ? N2 C2E 302 A 1 
HETATM 22 N N3 C2E . . . H 2 -23.46 -12.048 -93.563 1 100.91 ? N3 C2E 302 A 1 
HETATM 23 C C4 C2E . . . H 2 -24.385 -13.041 -93.647 1 103.67 ? C4 C2E 302 A 1 
HETATM 24 P P11 C2E . . . H 2 -27.368 -10.894 -88.803 1 84.12 ? P11 C2E 302 A 1 
HETATM 25 O O21 C2E . . . H 2 -26.892 -9.673 -89.557 1 82.73 ? O21 C2E 302 A 1 
HETATM 26 O O11 C2E . . . H 2 -27.923 -10.718 -87.409 1 85.33 ? O11 C2E 302 A 1 
HETATM 27 O O5A C2E . . . H 2 -28.59 -11.582 -89.579 1 81.73 ? O5A C2E 302 A 1 
HETATM 28 C C5A C2E . . . H 2 -29.755 -11.921 -88.789 1 78.25 ? C5A C2E 302 A 1 
HETATM 29 C C4A C2E . . . H 2 -30.726 -12.649 -89.673 1 77.13 ? C4A C2E 302 A 1 
HETATM 30 O O4A C2E . . . H 2 -31.518 -11.678 -90.397 1 73.8 ? O4A C2E 302 A 1 
HETATM 31 C C3A C2E . . . H 2 -30.049 -13.518 -90.72 1 78.53 ? C3A C2E 302 A 1 
HETATM 32 O O3A C2E . . . H 2 -29.813 -14.811 -90.164 1 83.1 ? O3A C2E 302 A 1 
HETATM 33 C C2A C2E . . . H 2 -31.098 -13.512 -91.81 1 77.8 ? C2A C2E 302 A 1 
HETATM 34 O O2A C2E . . . H 2 -32.048 -14.476 -91.445 1 78.79 ? O2A C2E 302 A 1 
HETATM 35 C C1A C2E . . . H 2 -31.683 -12.106 -91.726 1 75.9 ? C1A C2E 302 A 1 
HETATM 36 N N91 C2E . . . H 2 -31.055 -11.154 -92.634 1 76.19 ? N91 C2E 302 A 1 
HETATM 37 C C81 C2E . . . H 2 -30.077 -10.227 -92.357 1 74.97 ? C81 C2E 302 A 1 
HETATM 38 N N71 C2E . . . H 2 -29.714 -9.51 -93.396 1 74.65 ? N71 C2E 302 A 1 
HETATM 39 C C51 C2E . . . H 2 -30.509 -10.01 -94.424 1 78.5 ? C51 C2E 302 A 1 
HETATM 40 C C61 C2E . . . H 2 -30.568 -9.637 -95.786 1 80.8 ? C61 C2E 302 A 1 
HETATM 41 O O61 C2E . . . H 2 -29.904 -8.766 -96.37 1 81.76 ? O61 C2E 302 A 1 
HETATM 42 N N11 C2E . . . H 2 -31.537 -10.373 -96.467 1 83.47 ? N11 C2E 302 A 1 
HETATM 43 C C21 C2E . . . H 2 -32.32 -11.36 -95.925 1 84.53 ? C21 C2E 302 A 1 
HETATM 44 N N21 C2E . . . H 2 -33.172 -11.969 -96.76 1 90.4 ? N21 C2E 302 A 1 
HETATM 45 N N31 C2E . . . H 2 -32.252 -11.74 -94.654 1 81.09 ? N31 C2E 302 A 1 
HETATM 46 C C41 C2E . . . H 2 -31.336 -11.018 -93.968 1 78.38 ? C41 C2E 302 A 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           46 
#